Contacts of the helix formed by residues 135 - 152 (chain A) in PDB entry 4KM9
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 THR 135 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 5.3 4.7 - - + -
54A VAL* 4.3 13.6 - - + +
73A MET* 4.0 28.3 - - + -
133A PRO 4.2 3.8 - - - +
134A PRO* 1.3 74.4 - - + +
136A TRP* 1.3 65.1 + - - +
137A PRO* 3.2 3.8 - - - -
138A ALA* 3.2 18.1 + - - +
139A GLU* 3.4 6.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A PHE* 4.2 9.0 - + - -
124A LEU* 3.6 36.7 - - + +
134A PRO* 3.5 27.9 - - + +
135A THR* 1.3 79.2 + - - +
137A PRO* 1.4 88.5 - - + +
139A GLU* 3.2 10.9 + - + +
140A LEU* 3.0 29.0 + - + +
167A LEU* 3.9 15.2 - - + +
168A ASP* 3.5 56.4 - - + +
238A MET* 4.0 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A TYR* 3.6 25.8 - - + +
122A PHE* 3.7 31.0 - - + -
124A LEU* 4.4 2.2 - - + -
134A PRO 3.4 11.9 - - - +
135A THR 3.2 6.1 - - - -
136A TRP* 1.4 126.2 - - + +
138A ALA* 1.3 55.9 + - - +
140A LEU* 3.3 5.5 + - + +
141A MET* 3.0 34.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A VAL* 3.7 33.0 - - + -
71A VAL* 3.8 28.8 - - + +
73A MET* 4.8 4.9 - - - -
90A TYR* 4.5 2.4 - - + -
135A THR 3.2 12.9 + - - +
137A PRO* 1.3 80.4 - - - +
139A GLU* 1.3 56.8 + - - +
141A MET* 3.4 6.5 + - - +
142A GLN* 3.1 32.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A VAL* 5.7 5.2 - - - +
66A ASP* 4.7 7.3 - - - +
135A THR 3.4 5.6 + - - +
136A TRP* 3.2 15.1 + - - +
138A ALA* 1.3 77.2 - - - +
140A LEU* 1.3 63.8 + - - +
142A GLN* 3.4 14.9 - - - +
143A GLY* 3.2 17.0 + - - -
146A ARG* 4.7 12.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A TRP* 3.0 21.9 + - + +
137A PRO* 3.3 12.7 + - + +
139A GLU* 1.3 74.1 - - - +
141A MET* 1.3 59.9 + - + +
143A GLY* 3.1 3.6 + - - +
144A LEU* 2.8 32.5 + - + +
163A TRP* 4.9 14.0 - - + +
167A LEU* 5.0 11.7 - - + +
177A MET* 6.0 6.1 - - - -
200A ILE* 6.5 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LEU* 3.4 13.7 - - + +
71A VAL* 4.0 13.7 - - + -
90A TYR* 4.0 21.8 - - - +
91A ILE* 4.0 8.1 - - - +
92A SER* 3.5 24.9 - - - +
120A LEU* 3.5 40.2 - - + +
121A THR* 4.3 3.6 - - - +
122A PHE* 4.8 7.0 - - + -
137A PRO 3.0 19.9 + - - +
138A ALA* 3.6 6.5 - - - +
140A LEU* 1.3 76.4 - - + +
142A GLN* 1.3 56.3 + - - +
144A LEU* 3.7 8.5 - - - +
145A ALA* 2.9 30.3 + - - +
200A ILE* 4.2 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A VAL* 5.2 11.0 + - + +
55A THR 6.1 0.2 - - - -
56A ALA* 5.2 2.6 - - - +
66A ASP* 3.4 22.6 + - - +
67A PRO* 3.3 9.9 - - - +
68A LEU* 3.1 53.6 + - - +
71A VAL* 4.4 11.5 - - - +
138A ALA 3.1 19.9 + - - +
139A GLU* 3.4 17.7 - - - +
141A MET* 1.3 76.1 - - - +
143A GLY* 1.3 56.8 + - - +
145A ALA* 3.1 5.2 + - - +
146A ARG* 2.9 49.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A GLU 3.2 6.6 + - - -
140A LEU* 3.1 6.1 + - - -
142A GLN* 1.3 76.9 - - - +
144A LEU* 1.3 59.7 + - - +
146A ARG* 3.4 38.7 + - - +
147A TYR* 3.6 7.1 + - - +
163A TRP* 4.2 18.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A PHE* 6.1 0.2 - - + -
120A LEU* 3.8 19.5 - - + -
140A LEU* 2.8 17.5 + - + +
141A MET* 3.7 7.6 - - - +
143A GLY* 1.3 73.2 - - - +
145A ALA* 1.3 63.7 + - - +
147A TYR* 3.4 18.9 + - + +
148A VAL* 3.6 8.5 + - + +
155A PHE* 3.6 30.5 - - + -
161A VAL* 5.1 8.1 - - + -
163A TRP* 4.4 10.2 - - + -
177A MET* 3.6 38.4 - - + -
179A LEU* 5.4 3.4 - - + -
200A ILE* 3.8 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A PRO* 4.0 13.2 - - + -
68A LEU* 3.9 28.3 - - + -
95A LEU* 4.5 14.6 - - + -
120A LEU* 4.8 0.2 - - - +
141A MET 2.9 18.3 + - - +
142A GLN 3.1 4.5 + - - +
144A LEU* 1.3 74.3 - - - +
146A ARG* 1.3 64.3 + - - +
148A VAL* 3.2 9.4 + - - +
149A PHE* 3.1 31.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A TYR* 5.3 2.2 - - + -
65A PRO* 3.5 21.7 + - - +
66A ASP* 2.8 24.0 + - - -
67A PRO* 3.8 17.9 - - + +
139A GLU* 4.7 12.9 + - - +
142A GLN* 2.9 23.5 + - - +
143A GLY* 3.4 31.8 - - - +
144A LEU 3.2 0.2 - - - -
145A ALA* 1.3 76.7 - - - +
147A TYR* 1.3 60.7 + - - +
149A PHE* 4.3 1.9 - - - +
150A GLN* 3.0 46.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A GLY 3.6 6.4 + - - +
144A LEU* 3.4 11.7 + - - +
145A ALA 3.2 0.4 - - - -
146A ARG* 1.3 76.7 - - - +
148A VAL* 1.3 70.1 + - + +
150A GLN* 3.2 4.0 + - - -
151A SER* 2.8 52.1 + - - -
153A ASN* 2.8 34.5 + - + +
155A PHE* 4.2 29.6 - + + -
163A TRP* 6.4 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LEU* 3.8 14.6 - - + -
116A PHE* 3.5 34.5 - - + -
118A PHE* 4.4 12.1 - - + -
144A LEU* 3.7 15.9 - - + +
145A ALA* 3.2 8.2 + - - +
147A TYR* 1.3 79.2 - - + +
149A PHE* 1.3 54.0 + - - +
151A SER* 4.3 0.4 - - - -
152A GLU* 2.8 34.7 + - - -
153A ASN 3.5 19.3 - - - +
155A PHE* 3.8 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A TYR* 3.8 31.4 - + + +
67A PRO* 3.6 28.7 - - + -
68A LEU* 5.4 0.2 - - + -
94A GLY 3.9 10.8 - - - -
95A LEU* 3.7 27.1 - - + -
104A VAL* 3.7 28.5 - - + -
105A HIS* 3.6 29.4 - + - -
116A PHE* 3.9 11.3 - + - -
145A ALA* 3.1 28.0 + - + +
146A ARG* 4.3 2.0 - - - +
148A VAL* 1.3 78.9 - - - +
150A GLN* 1.3 61.2 + - - +
151A SER 3.2 1.9 + - - -
152A GLU* 3.8 15.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A TYR* 4.3 15.0 + - - +
146A ARG* 3.0 30.6 + - - +
147A TYR* 3.2 5.3 + - - +
149A PHE* 1.3 76.5 - - - +
151A SER* 1.3 59.5 + - - +
152A GLU* 5.4 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A TYR* 2.8 50.5 + - - -
150A GLN* 1.3 77.3 - - - +
152A GLU* 1.3 64.3 + - - +
153A ASN* 2.8 34.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A PHE* 3.8 25.2 - - + -
148A VAL 2.8 15.1 + - - -
149A PHE 3.9 12.8 - - - +
150A GLN 5.4 1.7 - - - +
151A SER* 1.3 77.9 - - - +
153A ASN* 1.3 63.8 + - - +
154A THR* 3.7 3.6 + - - +
----------------------------------------------------------
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