Contacts of the helix formed by residues 24 - 36 (chain C) in PDB entry 1V8C
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 24 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23C ALA* 1.3 85.9 - - + +
25C VAL* 1.3 65.6 + - - +
26C GLY* 3.5 2.4 + - - -
27C GLU* 3.1 35.0 + - - +
28C VAL* 3.1 24.3 + - - +
68C LEU 3.6 10.2 + - - -
69C SER* 4.3 11.7 - - - +
70C THR 3.3 12.6 - - - +
71C PRO* 4.5 4.5 - - + -
72C LEU* 3.3 6.7 - - - +
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Residues in contact with VAL 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C THR* 1.3 71.8 - - - +
26C GLY* 1.3 64.9 + - - +
28C VAL* 3.2 3.8 + - - +
29C LEU* 2.9 42.9 + - + +
49C LEU* 5.8 0.2 - - + -
55C VAL* 4.1 17.9 - - + -
57C LEU* 4.7 4.0 - - + -
62C VAL* 3.9 19.7 - - + -
67C GLY 3.8 14.8 - - - +
68C LEU* 3.6 5.1 + - + -
70C THR* 2.9 37.0 + - + +
72C LEU* 3.8 4.5 - - + +
78C LEU* 4.1 22.6 - - + +
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Residues in contact with GLY 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C THR* 4.0 0.7 - - - -
25C VAL* 1.3 78.0 - - - +
27C GLU* 1.3 55.4 + - - +
29C LEU* 3.3 3.0 + - - +
30C GLU* 2.8 43.2 + - - +
44C PHE* 4.5 1.5 - - - -
68C LEU* 2.8 42.7 + - - -
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Residues in contact with GLU 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C PRO 4.3 2.2 - - - -
22C GLY* 3.7 10.4 - - - -
23C ALA* 2.9 30.0 + - - +
24C THR* 3.1 31.1 + - - +
26C GLY* 1.3 75.8 - - - +
28C VAL* 1.3 63.4 + - - +
30C GLU* 3.4 10.8 + - - +
31C ASN* 3.1 28.9 + - - +
34C ARG* 5.0 0.2 + - - -
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Residues in contact with VAL 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C PRO* 3.8 24.5 - - + -
3C VAL* 3.6 31.0 - - + -
20C LEU* 4.1 13.2 - - + +
21C PRO 3.6 17.7 - - - +
22C GLY* 3.7 10.3 - - - +
24C THR 3.1 14.1 + - - +
25C VAL 3.6 6.1 - - - +
27C GLU* 1.3 77.5 - - - +
29C LEU* 1.3 58.3 + - + +
31C ASN* 3.1 4.9 + - - +
32C LEU* 2.9 25.0 + - + +
72C LEU* 4.2 7.0 - - + -
78C LEU* 4.0 12.6 - - + -
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Residues in contact with LEU 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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3C VAL* 5.8 0.4 - - + -
25C VAL* 2.9 37.6 + - + +
26C GLY 3.8 1.3 - - - +
28C VAL* 1.3 75.9 - - + +
30C GLU* 1.3 65.8 + - - +
32C LEU* 3.2 8.1 + - + +
33C VAL* 3.1 26.2 + - - +
43C LEU* 4.3 14.9 - - + +
44C PHE* 3.7 18.6 - - + -
49C LEU* 3.8 17.3 - - + -
55C VAL* 4.4 6.5 - - + -
68C LEU* 3.8 18.6 - - + -
78C LEU* 4.8 8.1 - - + -
80C LEU* 3.7 38.8 - - + -
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Residues in contact with GLU 30 (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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26C GLY* 2.8 26.0 + - - +
27C GLU* 3.7 10.7 + - - +
29C LEU* 1.3 76.1 - - - +
31C ASN* 1.3 62.2 + - - +
33C VAL* 3.4 5.2 + - - +
34C ARG* 3.1 50.6 + - - +
44C PHE* 4.1 20.8 - - + -
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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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20C LEU* 4.3 7.6 - - + -
21C PRO* 3.0 40.3 + - - +
22C GLY* 4.4 1.2 - - - +
27C GLU* 3.1 15.8 + - - +
28C VAL 3.5 7.4 - - - +
30C GLU* 1.3 75.7 - - - +
32C LEU* 1.3 63.7 + - - +
34C ARG* 3.1 28.5 + - - +
35C ALA* 3.0 23.4 + - - +
138D LEU* 3.6 24.8 - - + +
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Residues in contact with LEU 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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3C VAL* 4.5 5.2 - - + -
5C LEU* 4.2 9.0 - - + -
9C PHE* 6.4 0.2 - - + -
18C LEU* 3.6 31.0 - - + -
20C LEU* 3.6 13.9 - - + +
28C VAL* 2.9 14.1 + - + +
29C LEU* 3.2 13.4 + - + +
31C ASN* 1.3 77.2 - - - +
33C VAL* 1.3 56.7 + - - +
35C ALA* 3.2 2.9 + - + +
36C TYR* 2.9 29.9 + - + +
39C LEU* 3.7 22.9 - - + -
43C LEU* 3.5 17.0 - - + -
80C LEU* 3.3 33.9 - - + -
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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
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29C LEU 3.1 15.9 + - - +
30C GLU* 3.8 5.4 - - - +
31C ASN 3.3 0.2 - - - -
32C LEU* 1.3 73.9 - - - +
34C ARG* 1.3 60.8 + - + +
36C TYR 3.8 5.2 - - - -
37C PRO* 3.0 29.3 - - + +
39C LEU* 4.3 0.9 - - - -
40C LYS* 3.5 42.6 - - + +
43C LEU* 4.0 15.7 - - + -
44C PHE* 3.7 26.7 - - + -
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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
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30C GLU* 3.1 51.5 + - - +
31C ASN* 3.1 34.2 + - - +
33C VAL* 1.3 79.1 - - + +
35C ALA* 1.3 62.3 + - - +
37C PRO* 3.9 6.3 - - - +
137D SER* 3.5 21.6 - - - +
138D LEU* 4.0 20.6 - - + -
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Residues in contact with ALA 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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20C LEU* 4.7 1.8 - - + -
31C ASN 3.0 13.3 + - - +
32C LEU* 3.2 8.7 + - + +
34C ARG* 1.3 78.7 - - - +
36C TYR* 1.3 80.9 + - + +
37C PRO* 3.7 4.8 - - - +
135D VAL* 3.0 32.8 - - + +
136D GLY* 3.5 3.3 - - - -
137D SER* 2.9 20.6 + - - -
138D LEU* 3.6 12.1 - - + +
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Residues in contact with TYR 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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12C LEU 4.6 4.5 - - - +
13C THR* 3.6 56.2 + - + -
15C LYS* 3.9 23.0 + - + +
18C LEU* 3.6 29.4 - - + +
32C LEU* 2.9 12.5 + - + +
33C VAL* 3.2 8.9 - - - +
35C ALA* 1.3 97.1 - - + +
37C PRO* 1.3 61.4 - - - +
38C ALA* 3.1 6.1 - - + +
39C LEU* 2.9 31.5 + - + +
135D VAL* 4.2 5.6 - - + +
136D GLY* 3.9 21.0 + - - -
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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
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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