Contacts of the helix formed by residues 24 - 36 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C ARG 6.0 0.4 - - - +
22D GLY 3.4 0.2 - - - -
23D ALA* 1.3 85.5 - - + +
25D VAL* 1.3 65.0 + - - +
26D GLY* 3.6 2.6 + - - -
27D GLU* 3.1 31.1 + - + +
28D VAL* 3.1 23.6 + - - +
68D LEU 3.6 11.2 + - - -
69D SER* 3.9 15.9 - - - +
70D THR 3.1 10.5 - - - +
71D PRO* 4.4 5.2 - - + -
72D LEU* 3.8 7.0 - - - +
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Residues in contact with VAL 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D THR* 1.3 72.0 - - - +
26D GLY* 1.3 59.3 + - - +
28D VAL* 3.3 1.9 + - - +
29D LEU* 2.9 49.3 + - + +
55D VAL* 4.2 17.5 - - + -
57D LEU* 5.1 0.2 - - + -
62D VAL* 4.1 17.9 - - + -
67D GLY 3.7 13.9 - - - +
68D LEU* 3.6 8.3 + - + -
70D THR* 2.9 34.1 + - + +
72D LEU* 3.8 26.2 - - + +
78D LEU* 4.2 7.4 - - + -
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Residues in contact with GLY 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B GLU* 5.4 2.5 - - - -
24D THR* 4.0 0.9 - - - -
25D VAL* 1.3 76.5 - - - +
27D GLU* 1.3 55.5 + - - +
29D LEU* 3.3 2.2 + - - +
30D GLU* 2.8 42.6 + - - +
44D PHE* 5.6 0.7 - - - -
68D LEU* 2.8 43.3 + - - -
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Residues in contact with GLU 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C ARG 5.2 3.3 - - - +
22D GLY* 3.5 11.3 - - - -
23D ALA* 2.8 33.6 + - - +
24D THR* 3.1 26.2 + - + +
26D GLY* 1.3 74.2 - - - +
28D VAL* 1.3 62.9 + - - +
30D GLU* 3.3 15.0 + - - +
31D ASN* 3.0 32.2 + - - +
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Residues in contact with VAL 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D PRO* 3.8 16.4 - - + -
3D VAL* 3.6 31.6 - - + -
20D LEU* 4.0 13.6 - - + +
21D PRO 3.6 17.9 - - - +
22D GLY* 3.8 9.0 - - - +
24D THR 3.1 14.1 + - - +
25D VAL 3.6 6.1 - - - +
27D GLU* 1.3 76.5 - - - +
29D LEU* 1.3 59.5 + - + +
31D ASN* 3.2 5.0 + - - +
32D LEU* 2.9 23.7 + - - +
72D LEU* 3.7 17.0 - - + -
78D LEU* 4.2 11.9 - - + -
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Residues in contact with LEU 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D VAL* 5.3 0.7 - - + -
25D VAL* 2.9 28.6 + - + +
26D GLY* 3.9 2.0 - - - +
28D VAL* 1.3 75.5 - - + +
30D GLU* 1.3 65.3 + - - +
32D LEU* 3.1 20.7 + - + +
33D VAL* 3.0 26.7 + - - +
43D LEU* 4.4 8.9 - - + +
44D PHE* 3.8 18.6 - - + -
49D LEU* 3.8 19.7 - - + -
55D VAL* 4.3 8.3 - - + -
68D LEU* 3.8 24.9 - - + -
78D LEU* 4.6 9.2 - - + -
80D LEU* 3.9 27.8 - - + -
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Residues in contact with GLU 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B GLU* 5.9 3.3 - - - +
26D GLY* 2.8 30.3 + - - +
27D GLU* 3.6 12.5 - - - +
29D LEU* 1.3 76.0 - - - +
31D ASN* 1.3 64.3 + - - +
33D VAL* 3.3 6.2 + - - +
34D ARG* 3.2 27.8 + - + +
44D PHE* 4.4 18.7 - - + -
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Residues in contact with ASN 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C LEU* 3.7 21.0 - - + +
20D LEU* 4.4 8.5 - - + -
21D PRO* 2.9 45.4 + - - +
22D GLY* 4.6 1.4 - - - -
27D GLU* 3.0 17.3 + - - +
28D VAL 3.5 7.4 - - - +
30D GLU* 1.3 76.3 - - - +
32D LEU* 1.3 60.8 + - - +
34D ARG* 3.2 24.7 + - - +
35D ALA* 2.9 29.1 + - - +
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Residues in contact with LEU 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D VAL* 4.5 8.1 - - + -
5D LEU* 4.1 19.7 - - + -
9D PHE* 6.4 0.4 - - + -
18D LEU* 3.8 28.9 - - + -
20D LEU* 3.6 15.7 - - + +
28D VAL* 2.9 15.1 + - + +
29D LEU* 3.1 22.9 + - + +
31D ASN* 1.3 77.7 - - - +
33D VAL* 1.3 57.6 + - - +
35D ALA* 3.2 2.8 + - + +
36D TYR* 2.9 29.1 + - + +
39D LEU* 3.6 24.0 - - + -
43D LEU* 3.5 25.1 - - + -
80D LEU* 4.8 2.5 - - + -
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Residues in contact with VAL 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D LEU 3.0 13.2 + - - +
30D GLU* 3.3 8.0 + - - +
32D LEU* 1.3 73.4 - - - +
34D ARG* 1.3 62.8 + - + +
36D TYR 4.0 5.4 - - - -
37D PRO* 2.9 32.7 - - + +
39D LEU* 4.6 1.1 - - + -
40D LYS* 3.7 47.1 - - + +
43D LEU* 4.3 11.0 - - + -
44D PHE* 3.6 30.1 - - + -
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Residues in contact with ARG 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C SER* 3.5 21.5 - - - +
138C LEU* 3.5 33.9 - - + +
139C SER* 4.8 7.1 + - - +
30D GLU* 3.2 16.8 + - + +
31D ASN* 3.2 21.0 + - - +
33D VAL* 1.3 79.6 - - + +
35D ALA* 1.3 62.0 + - - +
37D PRO* 3.8 6.9 - - - +
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Residues in contact with ALA 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C VAL* 3.4 32.5 - - + +
136C GLY* 3.6 1.0 - - - -
137C SER* 2.8 24.9 + - - -
138C LEU* 3.7 8.5 - - + +
20D LEU* 4.3 6.1 - - + -
31D ASN 2.9 12.9 + - - +
32D LEU* 3.5 10.3 - - + +
33D VAL 3.2 0.2 - - - -
34D ARG* 1.3 79.4 - - - +
36D TYR* 1.3 82.8 + - + +
37D PRO* 3.7 0.6 - - - +
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Residues in contact with TYR 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C VAL* 4.5 1.1 - - + +
136C GLY* 3.6 26.8 + - - -
12D LEU 4.8 3.8 - - - +
13D THR* 3.7 50.6 + - + -
15D LYS* 4.0 21.3 - - + +
18D LEU* 3.6 34.0 - - + +
32D LEU* 2.9 13.0 + - + +
33D VAL* 3.2 6.3 - - - +
35D ALA* 1.3 96.2 - - + +
37D PRO* 1.3 57.0 - - - +
38D ALA* 2.9 14.4 + - + +
39D LEU* 2.9 22.7 + - + +
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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