Contacts of the helix formed by residues 135 - 150 (chain C) in PDB entry 3C6Q
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 ALA 135 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C LYS* 4.2 13.5 - - - -
65C PRO 4.4 2.9 - - - +
66C SER* 3.6 14.6 - - - +
68C PRO* 4.5 0.4 - - - -
90C THR* 4.3 4.0 - - - +
132C SER* 3.3 12.8 + - - +
133C LEU 4.4 0.2 - - - +
134C THR* 1.3 79.6 + - - +
136C MET* 1.3 68.1 + - - +
137C ASN* 3.4 7.2 - - - +
138C SER* 3.1 12.5 + - - -
139C LEU* 3.2 11.3 + - - +
190C TYR* 3.4 25.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 136 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C PRO* 3.4 20.5 - - + +
90C THR* 3.3 7.7 + - - +
91C ASP* 3.1 24.0 - - - +
93C PRO* 3.3 40.2 - - + -
134C THR 3.3 2.9 + - - +
135C ALA* 1.3 70.1 - - - +
137C ASN* 1.3 58.7 + - - +
138C SER 3.2 0.2 + - - -
139C LEU* 3.3 11.9 + - + +
140C GLN* 2.8 70.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 137 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C ASP* 3.5 12.6 + - - +
90C THR* 3.3 14.0 + - - +
105C ASN* 3.1 34.8 - - - +
135C ALA* 3.4 10.7 - - - +
136C MET* 1.3 75.2 - - - +
138C SER* 1.3 61.1 + - - -
140C GLN* 3.8 0.4 + - - -
141C ARG* 3.0 57.0 + - - +
190C TYR* 3.1 18.3 + - - -
500C XYP 2.9 31.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 138 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C THR* 2.7 25.0 + - - -
132C SER 3.4 15.9 + - - -
133C LEU* 5.3 0.2 - - - -
135C ALA* 3.1 8.0 + - - -
137C ASN* 1.3 78.0 + - - +
139C LEU* 1.3 68.4 + - - +
141C ARG* 3.3 2.4 + - - +
142C ILE* 3.1 30.6 + - - +
189C VAL* 3.7 13.1 - - - +
190C TYR* 3.4 25.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 139 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C PRO* 6.0 0.2 - - + -
133C LEU* 3.9 33.4 - - + +
134C THR* 3.7 24.2 - - - +
135C ALA 3.2 7.9 + - - +
136C MET* 3.6 13.5 - - + +
138C SER* 1.3 78.2 - - - +
140C GLN* 1.3 64.4 + - + +
142C ILE* 3.0 9.4 + - + +
143C GLN* 2.9 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 140 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C ASP* 5.3 5.3 + - - +
100C TYR* 5.8 0.3 - - - -
105C ASN* 2.9 42.2 + - + +
106C TYR* 3.8 21.3 - - + +
136C MET* 2.8 58.0 + - + +
137C ASN* 3.6 0.9 + - - -
139C LEU* 1.3 74.1 - - + +
141C ARG* 1.3 57.5 + - - +
143C GLN* 3.2 6.6 + - - +
144C GLY* 2.9 27.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 141 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C ASP* 4.3 1.8 + - - -
105C ASN* 2.9 43.6 + - + +
109C GLY* 3.4 6.8 - - - -
137C ASN* 3.0 37.9 + - - +
138C SER 3.3 3.8 + - - +
140C GLN* 1.3 74.4 - - - +
142C ILE* 1.3 57.8 + - - +
145C PHE* 3.1 27.4 + - - +
187C PHE* 4.1 4.1 - - + -
189C VAL* 2.9 36.0 + - + -
190C TYR* 4.6 0.8 - - - -
215C PHE* 3.2 48.6 - - + -
236C GLN* 2.9 25.6 + - - +
500C XYP 2.9 29.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 142 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C ILE* 4.2 28.7 - - + -
130C THR* 4.4 6.3 - - + -
133C LEU* 5.1 6.3 - - + -
138C SER* 3.1 30.5 + - - +
139C LEU* 3.0 8.8 + - + +
141C ARG* 1.3 76.5 - - - +
143C GLN* 1.3 61.6 + - - +
145C PHE* 3.8 4.3 - - - +
146C LYS* 2.8 53.9 + - + +
159C ILE* 4.2 19.7 - - + -
187C PHE* 4.9 0.9 - - + -
189C VAL* 3.8 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 143 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C TYR* 3.7 11.0 - - + -
139C LEU 2.9 13.0 + - - +
140C GLN* 3.7 9.4 - - - +
142C ILE* 1.3 76.9 - - - +
144C GLY* 1.3 56.6 + - - +
146C LYS* 3.3 15.9 + - - +
147C ASP* 2.9 68.5 + - - +
294D LYS* 3.4 31.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 144 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C TYR* 3.3 27.2 - - - -
109C GLY 4.1 0.4 - - - -
110C TYR* 3.3 29.8 - - - -
140C GLN 2.9 13.6 + - - -
143C GLN* 1.3 75.1 - - - +
145C PHE* 1.3 63.1 + - - +
148C ALA* 3.1 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 145 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C GLY 3.4 11.3 - - - +
113C GLY* 3.5 29.8 - - - -
116C MET* 3.9 23.6 - - + -
126C VAL* 4.0 25.4 - - + -
128C ILE* 4.5 7.0 - - + -
141C ARG 3.1 21.0 + - - +
142C ILE 3.8 3.1 - - - +
143C GLN 3.3 0.2 - - - -
144C GLY* 1.3 76.0 - - - +
146C LYS* 1.3 66.5 + - - +
148C ALA* 3.4 1.7 + - - +
149C ILE* 3.3 35.6 + - + +
154C ILE* 5.7 0.2 - - + -
156C ILE* 4.0 30.5 - - + -
187C PHE* 3.6 45.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 146 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C ILE* 2.8 41.1 + - + +
143C GLN* 3.5 18.0 + - - +
145C PHE* 1.3 75.1 - - + +
147C ASP* 1.3 56.4 + - - +
149C ILE* 3.2 10.8 - - - +
150C LYS* 2.8 36.2 + - - +
156C ILE* 3.6 24.7 - - + -
159C ILE* 4.3 21.0 - - - +
294D LYS* 5.9 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 147 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C TYR* 2.6 34.6 + - - +
110C TYR* 4.0 10.0 + - + -
143C GLN* 2.9 41.8 + - - +
144C GLY 3.9 1.8 - - - +
146C LYS* 1.3 72.9 - - - +
148C ALA* 1.3 67.6 + - - +
150C LYS* 3.2 38.9 + - - +
151C ASP* 4.3 2.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 148 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C TYR* 3.5 50.9 + - + +
113C GLY* 4.0 1.6 - - - -
114C LEU* 3.7 21.9 - - + +
117C LYS* 4.4 7.2 + - - +
144C GLY 3.1 16.4 + - - +
145C PHE 3.7 4.9 - - - +
147C ASP* 1.3 79.0 - - - +
149C ILE* 1.3 58.8 + - - +
151C ASP* 4.2 13.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 149 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C GLY* 3.8 26.2 - - - +
116C MET* 5.1 0.4 - - + -
117C LYS* 4.7 10.3 - - + +
145C PHE* 3.3 28.0 + - + +
146C LYS* 3.2 14.3 + - - +
148C ALA* 1.3 73.1 - - - +
150C LYS* 1.3 57.4 + - - +
151C ASP* 2.8 13.8 + - - -
152C SER* 2.8 34.3 + - - +
154C ILE* 3.5 45.5 - - + +
156C ILE* 3.7 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 150 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C LYS* 2.8 15.8 + - - +
147C ASP* 3.2 33.5 + - - +
149C ILE* 1.3 78.0 - - - +
151C ASP* 1.3 61.3 + - - +
152C SER 3.6 3.8 + - - +
154C ILE 5.9 0.4 - - - -
297D GLU* 3.0 33.8 + - + +
----------------------------------------------------------
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