Contacts of the helix formed by residues 26 - 40 (chain C) in PDB entry 2NVT
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 ASP 26 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25C VAL* 1.3 82.6 - - - +
27C LEU* 1.3 69.1 + - - +
28C ALA* 3.3 28.2 + - - +
29C MET* 3.3 22.3 + - + +
30C ALA 3.6 2.4 + - - -
224C GLN* 5.1 6.2 - - - +
225C ALA 4.6 2.8 - - - +
228C PHE* 4.2 3.1 - - - -
45K LEU* 5.9 0.2 - - - +
48K ALA* 3.6 13.6 - - - +
49K GLU* 5.1 10.5 - - - +
52K ASN* 4.8 15.0 + - - +
97K LYS* 5.4 7.5 - - + +
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Residues in contact with LEU 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1077B THR* 3.3 45.1 - - + +
1078B GLY 4.0 6.1 - - - +
1079B LYS* 4.4 4.9 - - + +
26C ASP* 1.3 76.6 + - - +
28C ALA* 1.3 60.5 + - + +
29C MET 2.6 12.8 + - - -
30C ALA* 3.1 12.0 + - - +
31C ASN* 3.3 9.5 + - + +
178C PHE* 5.7 0.9 - - + -
180C TYR* 3.5 35.9 - - + +
188C HIS* 6.0 0.4 - - + -
225C ALA* 3.7 32.4 + - + -
228C PHE* 3.3 23.7 - - + -
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Residues in contact with ALA 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C ASP* 3.3 7.4 + - - +
27C LEU* 1.3 81.9 - - + +
29C MET* 1.3 56.6 + - - +
31C ASN* 4.3 2.7 - - - -
32C SER* 3.1 25.9 + - - -
44K ASN* 3.8 30.3 + - - +
45K LEU* 3.5 12.1 - - + +
48K ALA* 3.3 34.5 - - + -
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Residues in contact with MET 29 (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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6C PRO* 5.0 3.1 - - - -
25C VAL* 3.5 22.2 - - + -
26C ASP* 3.4 17.9 - - + +
27C LEU 2.6 6.3 + - - -
28C ALA* 1.3 74.2 - - - +
30C ALA* 1.3 67.2 + - - +
31C ASN 3.0 1.3 + - - -
32C SER* 3.2 4.0 + - - -
33C LEU* 2.8 27.0 + - + +
251C LEU* 4.7 1.5 - - + +
45K LEU* 3.5 28.9 - - + -
49K GLU* 4.1 13.9 - - - +
94K ILE* 4.4 14.8 - - + +
97K LYS* 4.4 20.6 - - + -
98K LEU* 3.4 37.2 - - + -
101K LEU* 6.4 1.1 - - - -
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Residues in contact with ALA 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C LEU* 4.6 10.8 - - + -
25C VAL* 4.6 2.7 - - + +
26C ASP 3.6 3.5 + - - +
27C LEU 3.1 7.5 + - - +
29C MET* 1.3 80.7 - - - +
31C ASN* 1.3 63.7 + - - +
33C LEU* 3.2 8.8 - - - +
34C ARG* 3.1 19.8 + - - +
178C PHE* 3.9 12.3 - - + -
228C PHE* 4.0 20.4 - - + -
230C MET* 3.7 27.3 - - + +
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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
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1075B GLY 3.1 9.4 + - - +
1076B HIS 2.8 27.0 + - - +
1077B THR 3.0 25.0 - - - +
1078B GLY* 3.2 15.1 - - - -
27C LEU 3.3 8.9 + - - +
28C ALA 4.5 4.3 - - - +
29C MET 3.0 1.2 - - - -
30C ALA* 1.3 75.7 - - - +
32C SER* 1.3 54.4 + - - +
33C LEU 2.5 16.1 + - - -
34C ARG* 2.7 38.5 + - - +
35C ARG* 2.9 33.1 + - - +
178C PHE* 4.3 7.7 - - + -
44K ASN* 5.1 1.1 - - - +
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Residues in contact with SER 32 (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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28C ALA 3.1 20.2 + - - -
29C MET 3.2 4.4 + - - -
31C ASN* 1.3 76.5 - - - +
33C LEU* 1.3 60.2 + - - +
35C ARG* 3.9 11.9 - - - +
36C VAL* 3.4 17.8 + - - +
251C LEU* 3.3 22.3 - - - +
40K HIS 3.9 5.4 + - - -
41K THR* 2.5 30.9 + - - +
44K ASN* 5.0 1.7 + - - +
45K LEU* 3.4 16.3 + - - +
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Residues in contact with LEU 33 (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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20C PHE* 5.9 4.0 - - + -
22C LEU* 5.5 10.5 - - + -
29C MET* 2.8 14.2 + - + +
30C ALA* 3.2 14.4 - - - +
31C ASN 2.5 6.9 + - - -
32C SER* 1.3 69.1 - - - +
34C ARG* 1.3 55.3 + - - +
35C ARG 2.8 4.5 + - - -
36C VAL* 2.8 5.4 + - - +
37C MET* 2.7 67.3 + - + +
230C MET* 5.7 6.3 - - + -
244C VAL* 5.4 2.0 - - + -
247C GLY 4.9 0.9 - - - -
248C ILE* 3.9 37.5 - - + +
251C LEU* 3.8 19.3 - - + +
98K LEU* 5.0 7.4 - - + -
101K LEU* 5.2 6.3 - - + -
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Residues in contact with ARG 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
996B ARG* 3.5 22.6 + - - +
997B GLU* 3.7 14.2 + - - +
999B MET 4.1 4.9 + - - -
1001B PHE* 3.4 49.6 - - - +
1075B GLY 3.3 16.1 + - - -
30C ALA 3.1 8.8 + - - +
31C ASN* 2.7 23.1 + - - +
33C LEU* 1.3 76.0 - - - +
35C ARG* 1.3 88.7 + - - +
37C MET* 3.4 14.1 - - - +
38C ILE* 3.1 37.9 + - + +
176C ILE* 4.2 23.7 + - + +
178C PHE* 4.3 16.6 - - + -
230C MET* 5.6 3.5 - - - -
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Residues in contact with ARG 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
997B GLU* 2.8 30.3 + - + +
998B ASP* 2.6 32.1 + - - +
1075B GLY 3.5 4.2 + - - -
1076B HIS* 3.8 11.8 + - - +
31C ASN* 3.0 36.0 - - - +
32C SER* 3.9 15.7 - - - +
33C LEU 2.8 1.0 + - - -
34C ARG* 1.3 92.9 - - - +
36C VAL* 1.3 59.1 + - - +
38C ILE* 3.1 8.6 + - - +
39C ALA* 2.9 30.1 + - - +
40C GLU* 5.5 0.4 - - - -
39K ASP* 4.2 4.6 + - - -
40K HIS* 4.1 13.4 - - - +
41K THR* 2.3 55.0 + - - +
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Residues in contact with VAL 36 (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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32C SER 3.4 7.8 + - - +
33C LEU* 2.8 10.9 + - - +
35C ARG* 1.3 69.1 - - - +
37C MET* 1.3 65.1 - - - +
39C ALA 3.1 0.2 + - - -
40C GLU* 2.7 55.7 + - + +
41C ILE* 3.6 9.3 + - + -
247C GLY 3.7 22.4 - - - +
250C THR* 3.8 17.3 - - - -
251C LEU* 4.2 19.3 - - + +
254C LYS* 5.0 3.8 - - + -
41K THR* 3.3 25.1 - - + +
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Residues in contact with MET 37 (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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20C PHE* 5.9 0.9 - - - -
33C LEU* 2.7 59.5 + - + +
34C ARG* 3.4 11.7 - - - +
36C VAL* 1.3 73.4 - - - +
38C ILE* 1.3 62.5 + - - +
41C ILE* 3.8 23.8 - - - +
172C PRO* 3.9 0.9 - - - +
173C ALA* 3.4 13.7 - - + +
176C ILE* 3.9 16.6 - - + -
230C MET* 6.1 2.7 - - - +
232C VAL* 3.8 28.9 - - + -
243C VAL* 3.8 22.4 - - + +
244C VAL* 3.9 27.1 - - + +
247C GLY* 4.4 4.7 - - - -
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Residues in contact with ILE 38 (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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844B SER* 5.3 1.8 - - - +
996B ARG* 3.4 53.9 + - + +
997B GLU* 3.6 31.9 - - + +
34C ARG* 3.1 27.4 - - + +
35C ARG* 3.1 9.2 + - - +
37C MET* 1.3 81.2 - - - +
39C ALA* 1.3 63.9 + - - +
164C ALA* 3.2 16.7 - - + +
171C GLY* 4.0 11.3 - - - -
172C PRO* 4.1 0.7 - - - +
173C ALA* 3.8 7.3 - - + +
174C ALA 4.1 4.0 - - - +
176C ILE* 3.7 25.6 - - + +
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Residues in contact with ALA 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
997B GLU* 3.4 38.1 - - + +
35C ARG 2.9 9.9 + - - +
38C ILE* 1.3 75.7 - - - +
40C GLU* 1.3 67.8 + - + +
41C ILE 3.9 1.1 - - - -
163C ILE* 3.5 3.3 - - - +
164C ALA* 3.1 33.9 + - + -
165C LYS* 3.2 23.4 + - + +
172C PRO* 6.0 0.4 - - - -
41K THR* 6.1 0.4 - - - +
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Residues in contact with GLU 40 (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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35C ARG 5.4 0.2 - - - +
36C VAL* 2.7 35.6 + - + -
38C ILE 3.8 0.2 - - - -
39C ALA* 1.3 86.4 - - + +
41C ILE* 1.3 62.7 + - - +
42C PRO* 3.6 7.3 - - - +
163C ILE* 3.5 18.9 - - + +
165C LYS* 3.4 30.5 + - + +
250C THR* 3.7 15.2 - - + +
254C LYS* 2.6 39.8 + - - +
38K GLU* 5.4 0.2 - - - +
39K ASP* 4.8 0.3 - - - +
41K THR* 3.5 27.4 + - - +
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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
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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