Contacts of the helix formed by residues 137 - 159 (chain L) in PDB entry 5JKL
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TYR 137 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27L GLU* 4.2 8.1 - - - -
65L HIS* 2.7 53.5 + + + -
68L LYS* 3.4 21.5 - - + +
69L LEU* 3.4 21.1 - - + +
114L LEU* 3.9 34.3 - - + -
132L PHE* 3.4 34.3 - + - -
133L ILE* 2.9 18.9 + - + +
135L THR 3.6 0.6 - - - -
136L HIS* 1.3 96.1 - - + +
138L LEU* 1.3 63.6 + - - +
139L ASN 3.4 2.2 - - - -
140L GLU* 3.3 5.3 + - + +
141L GLN* 3.0 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 138 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111L ASN* 4.4 6.9 - - - +
114L LEU* 4.0 22.4 - - + +
115L LEU* 4.1 26.9 - - + -
118L HIS* 4.4 9.2 - - + -
133L ILE* 2.9 39.8 + - + +
134L GLU* 3.8 30.2 + - + +
137L TYR* 1.3 73.1 - - - +
139L ASN* 1.3 58.8 + - - +
141L GLN* 3.4 6.5 + - - +
142L VAL* 3.1 30.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 139 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134L GLU 4.1 8.6 + - - +
135L THR 5.8 2.7 - - - +
136L HIS 5.6 0.2 - - - -
137L TYR 3.4 0.4 - - - -
138L LEU* 1.3 75.5 - - - +
140L GLU* 1.3 63.9 + - - +
142L VAL* 4.0 17.1 - - - +
143L LYS* 2.9 57.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 140 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61L GLU* 5.0 8.0 - - - +
65L HIS* 4.9 21.4 + - + +
135L THR 5.5 2.5 - - - +
136L HIS* 3.3 25.8 - - - +
137L TYR* 3.3 9.3 + - + +
138L LEU 3.3 0.2 - - - -
139L ASN* 1.3 80.8 + - - +
141L GLN* 1.3 58.8 + - - +
143L LYS* 2.9 36.0 + - - +
144L ALA* 3.0 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 141 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65L HIS* 4.8 7.1 - - - -
107L GLU* 2.8 53.1 + - - +
110L VAL* 3.8 12.1 - - - +
111L ASN* 3.4 25.4 - - + +
114L LEU* 3.4 31.3 - - + +
137L TYR* 3.0 14.4 + - - +
138L LEU 3.6 4.5 - - - +
139L ASN 3.2 0.2 - - - -
140L GLU* 1.3 75.8 - - - +
142L VAL* 1.3 60.5 + - - +
144L ALA* 3.3 2.7 + - - +
145L ILE* 2.9 36.7 + - + +
201L FE 3.9 14.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 142 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111L ASN* 5.1 10.8 - - - +
138L LEU* 3.1 20.8 + - + +
139L ASN* 3.3 18.4 + - - +
141L GLN* 1.3 74.5 - - - +
143L LYS* 1.3 66.6 + - + +
145L ILE* 3.5 7.0 + - + +
146L LYS* 3.0 25.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 143 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139L ASN* 2.9 42.8 + - - +
140L GLU* 2.9 37.5 + - - +
142L VAL* 1.3 77.7 - - + +
144L ALA* 1.3 57.1 + - - +
146L LYS* 3.5 5.5 + - - +
147L GLU* 3.0 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 144 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58L GLN* 5.8 3.4 - - - +
107L GLU* 4.1 27.6 - - + +
140L GLU 3.0 19.4 + - - +
141L GLN* 3.3 5.1 + - - +
143L LYS* 1.3 74.7 - - - +
145L ILE* 1.3 59.8 + - - +
147L GLU* 3.4 5.8 + - - +
148L LEU* 3.0 37.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 145 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104L LEU* 3.8 22.2 - - + +
107L GLU* 3.8 36.1 - - + +
108L LYS* 3.9 28.3 - - + -
111L ASN* 3.9 25.1 - - + +
141L GLN 2.9 22.7 + - - +
142L VAL* 3.9 6.3 - - + +
144L ALA* 1.3 74.2 - - - +
146L LYS* 1.3 58.4 + - - +
148L LEU* 3.4 1.7 + - - -
149L GLY* 2.9 27.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 146 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142L VAL* 3.0 20.6 + - + +
143L LYS* 3.8 6.3 - - - +
145L ILE* 1.3 75.6 - - - +
147L GLU* 1.3 58.0 + - - +
149L GLY* 3.4 2.1 + - - +
150L ASP* 3.0 67.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 147 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54L TYR* 2.8 32.2 + - - +
58L GLN* 4.1 6.1 + - - -
143L LYS 3.0 19.0 + - - +
144L ALA* 3.8 6.0 - - - +
146L LYS* 1.3 75.3 - - - +
148L LEU* 1.3 64.4 + - - +
150L ASP* 3.3 11.3 + - - +
151L HIS* 3.0 44.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 148 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34L TYR* 3.9 7.4 - - - +
54L TYR* 3.7 24.7 - - + +
55L PHE* 5.1 0.2 - - + -
100L MET* 3.7 26.7 - - - +
103L ALA* 3.6 30.1 - - + +
104L LEU* 3.8 15.7 - - + +
107L GLU* 3.6 30.5 - - + -
144L ALA* 3.0 23.2 + - + +
145L ILE* 4.0 3.1 - - - +
147L GLU* 1.3 79.8 - - - +
149L GLY* 1.3 56.0 + - - +
151L HIS* 3.2 4.1 + - - +
152L VAL* 2.9 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 149 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104L LEU* 4.2 16.9 - - - +
145L ILE 2.9 17.3 + - - -
146L LYS* 3.8 1.1 - - - -
148L LEU* 1.3 76.2 - - - +
150L ASP* 1.3 61.9 + - - +
152L VAL* 3.3 4.2 + - - +
153L THR* 2.9 29.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 150 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146L LYS* 3.0 60.3 + - - +
147L GLU* 3.4 10.7 - - - +
149L GLY* 1.3 75.9 - - - +
151L HIS* 1.3 61.1 + - + +
153L THR* 3.4 6.3 + - - -
154L ASN* 3.0 41.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 151 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54L TYR* 3.8 21.6 + - - -
100L MET* 3.9 31.9 - - + -
147L GLU* 3.0 41.4 + - + +
148L LEU* 3.6 6.7 - - - +
150L ASP* 1.3 79.0 - - + +
152L VAL* 1.3 58.4 + - - +
154L ASN* 3.4 2.0 + - - +
155L LEU* 2.9 36.0 + - - +
170L PHE* 3.6 23.5 - + + -
174L THR* 3.7 23.1 - - + +
175L LEU* 3.9 11.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 152 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97L LEU* 3.9 9.1 - - + +
100L MET* 3.8 34.7 - - + +
101L GLU* 3.9 15.0 - - + +
104L LEU* 4.4 13.2 - - + -
148L LEU 2.9 21.9 + - - +
149L GLY* 3.6 6.5 - - - +
151L HIS* 1.3 74.8 - - - +
153L THR* 1.3 64.8 + - - +
155L LEU* 3.3 1.4 + - - +
156L ARG* 2.9 65.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 153 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149L GLY 2.9 18.9 + - - -
150L ASP* 3.6 7.4 - - - +
151L HIS 3.3 0.2 - - - -
152L VAL* 1.3 79.5 - - - +
154L ASN* 1.3 62.2 + - - +
156L ARG* 3.4 11.4 + - - +
157L LYS* 2.9 50.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 154 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150L ASP* 3.0 33.6 + - - +
151L HIS* 4.9 1.2 + - - +
153L THR* 1.3 81.1 - - - +
155L LEU* 1.3 63.2 + - - +
157L LYS* 3.2 5.6 + - - +
158L MET* 3.0 37.7 + - - +
170L PHE* 3.9 24.3 - - + -
174L THR* 5.7 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 155 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51L PHE* 4.1 7.2 - - + -
97L LEU* 4.0 26.2 - - + +
100L MET* 3.9 27.4 - - + -
151L HIS 2.9 20.2 + - - +
152L VAL 3.8 2.7 - - - +
154L ASN* 1.3 76.2 - - - +
156L ARG* 1.3 61.2 + - - +
158L MET* 3.3 4.5 + - - +
159L GLY 3.3 4.9 + - - -
160L ALA* 2.9 33.6 + - + +
166L ALA 4.4 2.5 - - - +
167L GLU* 4.1 27.6 - - + +
170L PHE* 3.6 44.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 156 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97L LEU* 4.0 17.4 - - + +
101L GLU* 2.9 29.3 + - - +
104L LEU* 6.3 0.6 - - - +
152L VAL* 2.9 40.3 + - - +
153L THR* 3.7 11.0 + - - +
155L LEU* 1.3 76.1 - - - +
157L LYS* 1.3 63.8 + - + +
159L GLY* 3.1 14.0 + - - -
160L ALA 4.2 9.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 157 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153L THR* 2.9 39.1 + - + +
154L ASN* 3.2 5.6 + - - +
156L ARG* 1.3 77.7 - - + +
158L MET* 1.3 61.0 + - + +
159L GLY* 3.5 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 158 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154L ASN* 3.0 32.6 + - + +
155L LEU* 3.8 4.9 - - - +
156L ARG 3.2 0.4 - - - -
157L LYS* 1.3 78.0 - - + +
159L GLY* 1.3 56.9 + - - +
160L ALA 3.7 0.2 - - - -
163L SER* 4.3 4.0 + - - -
166L ALA* 3.4 45.6 - - + +
169L LEU* 4.0 15.3 - - + -
170L PHE* 3.7 38.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 159 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156L ARG 3.1 11.5 + - - -
157L LYS 3.2 1.6 - - - -
158L MET* 1.3 78.6 - - - +
160L ALA* 1.3 65.6 + - - +
162L GLU* 3.5 6.4 + - - +
163L SER* 3.0 30.0 + - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il