Contacts of the helix formed by residues 22 - 39 (chain C) in PDB entry 3NT7
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 VAL 22 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C TRP* 3.1 28.0 - - + +
21C PRO* 1.3 81.0 - - + +
23C MET* 1.3 70.6 + - - +
24C SER 3.4 2.3 + - - -
25C GLN* 3.4 6.2 + - - +
26C LEU* 3.0 18.1 + - + +
143C LEU* 3.5 39.2 - - + +
144C LEU* 3.9 23.8 - - + -
147C HIS* 3.7 33.2 - - + +
150C LYS* 6.3 0.2 - - - +
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Residues in contact with MET 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C VAL* 3.8 23.8 - - + -
13C ILE* 3.8 16.6 - - + -
15C TYR* 3.5 59.0 - - + +
19C TRP* 3.5 19.1 - - - +
20C GLU* 3.3 9.9 + - - +
22C VAL* 1.3 83.8 - - - +
24C SER* 1.3 59.1 + - - +
26C LEU* 3.2 19.1 + - + +
27C VAL* 2.8 33.5 + - - +
53C LEU* 3.9 21.1 - - + -
144C LEU* 5.6 0.4 - - - -
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Residues in contact with SER 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C VAL* 6.2 0.7 - - - -
20C GLU 4.8 2.0 + - - -
21C PRO 5.3 2.1 + - - -
22C VAL 3.5 0.8 - - - -
23C MET* 1.3 77.7 - - - +
25C GLN* 1.3 63.2 + - - +
27C VAL* 3.5 8.7 + - - +
28C GLU* 3.2 24.5 + - - +
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Residues in contact with GLN 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C PRO 4.9 7.6 - - - +
22C VAL* 3.4 8.5 + - - +
23C MET 3.4 0.2 - - - -
24C SER* 1.3 78.8 + - - +
26C LEU* 1.3 58.9 + - - +
28C GLU* 3.4 14.7 + - - +
29C PHE* 2.9 49.4 + - + -
143C LEU* 3.4 31.3 - - + +
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Residues in contact with LEU 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C ILE* 4.0 27.4 - - + -
22C VAL 3.0 14.9 + - - +
23C MET* 3.2 29.1 + - + +
25C GLN* 1.3 71.8 - - - +
27C VAL* 1.3 60.2 + - + +
29C PHE* 3.2 2.7 + - - -
30C TYR* 2.7 39.2 + - + +
50C PHE* 4.1 20.6 - - + -
53C LEU* 5.2 0.9 - - + -
140C ILE* 3.3 43.5 - - + -
143C LEU* 3.6 9.4 - - + +
144C LEU* 4.7 14.4 - - + -
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Residues in contact with VAL 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C VAL* 3.6 38.4 - - + -
5C THR 3.8 15.5 - - - +
6C VAL* 4.1 15.7 - - + -
23C MET 2.8 20.1 + - - +
24C SER* 3.8 8.3 - - - +
26C LEU* 1.3 78.5 - - + +
28C GLU* 1.3 59.1 + - - +
30C TYR* 3.8 0.2 - - - -
31C ASN* 2.9 50.9 + - - +
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Residues in contact with GLU 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ASN* 5.8 0.2 - - - +
167A ARG* 5.7 3.0 + - - -
24C SER 3.2 15.0 + - - +
25C GLN* 3.7 16.7 - - - +
27C VAL* 1.3 82.5 - - - +
29C PHE* 1.3 67.6 + - + +
31C ASN* 3.9 6.3 + - - +
32C GLU* 3.3 29.7 + - + +
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Residues in contact with PHE 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C GLN* 2.9 40.7 + - + +
26C LEU 3.7 1.3 - - - +
28C GLU* 1.3 82.5 - - + +
30C TYR* 1.3 64.9 + - - +
32C GLU* 3.3 29.2 + - - +
33C VAL* 3.5 17.2 + - + +
139C LYS* 3.8 55.9 - - + -
140C ILE* 3.5 20.0 - - + -
143C LEU* 4.2 17.5 - - + -
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Residues in contact with TYR 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C VAL* 4.1 26.7 - - + -
8C HIS* 4.3 3.1 - - + -
9C ALA 2.5 31.2 + - - -
10C PRO* 3.4 11.9 - - + +
26C LEU* 2.7 28.7 + - + +
27C VAL* 3.9 4.5 - - - +
29C PHE* 1.3 73.5 - - - +
31C ASN* 1.3 58.9 + - - +
33C VAL* 3.3 2.1 + - + -
34C ALA* 3.0 48.1 + - + +
37C LEU* 4.0 15.0 - - + +
38C LEU* 4.2 2.4 - - - +
49C PHE* 3.6 15.4 - + - -
50C PHE* 3.4 34.3 - + - -
137C TRP* 4.0 19.7 - + - -
140C ILE* 4.0 10.3 - - + +
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Residues in contact with ASN 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C THR 5.3 0.2 + - - -
6C VAL* 3.4 14.6 - - - +
7C SER* 3.1 42.8 + - - +
8C HIS* 3.7 26.2 + - - -
27C VAL* 2.9 33.6 + - - +
28C GLU* 4.2 7.0 - - - +
29C PHE 3.4 0.2 - - - -
30C TYR* 1.3 77.3 - - - +
32C GLU* 1.3 62.9 + - + +
33C VAL 3.6 0.3 + - - -
34C ALA 4.3 0.7 + - - -
35C SER 5.5 0.2 + - - -
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Residues in contact with GLU 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ILE* 4.3 8.6 - - + +
28C GLU* 3.3 23.8 + - + +
29C PHE* 3.3 25.6 + - - +
30C TYR 3.2 0.8 - - - -
31C ASN* 1.3 80.0 - - + +
33C VAL* 1.3 64.5 - - + +
35C SER* 5.0 0.7 + - - -
36C TRP* 3.5 21.1 - - - -
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Residues in contact with VAL 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ILE* 4.0 22.0 - - + -
29C PHE 3.6 16.2 - - - +
30C TYR* 3.3 8.7 + - - +
32C GLU* 1.3 84.6 - - + +
34C ALA* 1.3 69.4 + - - +
35C SER 3.4 2.0 - - - -
36C TRP* 3.1 26.8 + - - +
37C LEU* 3.5 17.8 + - + +
135C ILE 5.6 0.7 - - - +
136C TYR* 3.6 39.5 - - + +
140C ILE* 4.3 9.4 - - + -
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Residues in contact with ALA 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C HIS* 3.6 34.3 - - + +
30C TYR* 3.0 36.9 + - + +
31C ASN 4.3 1.0 + - - -
32C GLU 3.7 1.2 - - - -
33C VAL* 1.3 77.4 - - - +
35C SER* 1.3 57.7 + - - +
37C LEU* 2.8 28.0 + - - +
38C LEU* 2.9 19.5 + - + +
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Residues in contact with SER 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C HIS* 4.6 20.3 + - - -
32C GLU 5.0 0.7 + - - -
33C VAL 3.4 0.4 - - - -
34C ALA* 1.3 76.5 - - - +
36C TRP* 1.3 85.8 + - - +
38C LEU* 3.5 8.8 + - - +
39C ARG* 3.3 23.2 + - - +
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Residues in contact with TRP 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ASP* 5.7 0.8 + - - -
131A LYS 4.5 8.1 - - - -
132A SER* 2.9 38.4 + - - -
133A HIS* 4.5 3.0 + - - -
134A ALA* 5.4 2.5 - - + -
135A ILE* 3.7 32.3 - - + -
136A TYR* 3.0 32.4 + + - -
32C GLU 3.5 24.0 - - - -
33C VAL* 3.1 11.9 + - - +
35C SER* 1.3 103.9 + - - +
37C LEU* 1.3 61.0 + - - +
39C ARG* 3.8 32.6 + - - +
40C ASP* 4.8 1.9 + - - +
133C HIS* 4.6 4.5 - - - -
136C TYR* 3.2 34.6 - + + -
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Residues in contact with LEU 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C TYR* 4.0 17.5 - - + -
33C VAL* 3.5 17.7 + - + +
34C ALA* 2.8 9.5 + - - +
36C TRP* 1.3 78.8 - - - +
38C LEU* 1.3 65.9 + - + +
39C ARG 3.3 0.7 + - - -
40C ASP 3.7 3.1 + - - +
42C THR* 3.3 26.9 - - - +
49C PHE* 4.6 8.1 - - + -
124C SER* 3.5 1.8 - - - +
133C HIS* 3.1 42.1 + - + -
136C TYR* 3.7 21.1 - - + -
137C TRP* 3.4 46.4 - - + +
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Residues in contact with LEU 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C HIS* 3.7 32.3 - - + -
9C ALA* 3.8 26.0 - - + +
30C TYR* 4.2 2.0 - - - +
34C ALA* 2.9 21.8 + - + +
35C SER* 4.0 5.6 - - - +
37C LEU* 1.3 75.9 - - + +
39C ARG* 1.3 65.4 + - - +
40C ASP 3.3 7.6 + - - +
42C THR* 5.5 0.2 - - - -
46C PRO* 3.7 37.2 - - + -
49C PHE* 4.2 12.3 - - + -
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Residues in contact with ARG 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A TRP* 5.0 2.8 + - - -
39A ARG* 3.5 39.6 - - - +
40A ASP* 2.9 36.0 + - - -
126A LYS* 4.2 18.1 - - - +
136A TYR* 4.0 8.1 + - - -
35C SER 3.3 15.7 + - - +
36C TRP* 3.8 24.2 + - - +
37C LEU 3.3 0.8 - - - -
38C LEU* 1.3 80.5 - - - +
40C ASP* 1.3 68.9 + - - +
136C TYR* 3.9 19.4 + - - -
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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) + - + + + + + -
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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