Contacts of the helix formed by residues 9 - 22 (chain D) in PDB entry 2X86
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 GLY 9 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6D GLY 2.7 14.2 + - - -
8D ALA* 1.3 79.1 - - - +
10D PHE* 1.3 57.6 + - - -
11D ILE 3.7 1.1 - - - -
13D SER* 2.7 34.7 + - - -
31D ASP* 3.2 4.5 + - - -
38D LYS* 4.9 0.2 - - - -
41D ASN* 4.2 0.7 - - - -
177D HIS* 3.9 10.1 - - - -
400D NAP 3.3 23.3 - - - -
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Residues in contact with PHE 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D GLY* 1.3 70.4 - - - -
11D ILE* 1.3 67.9 + - + +
13D SER* 3.0 9.4 + - - -
14D ASN* 2.8 28.7 + - - -
170D VAL* 3.6 32.8 - - + -
171D TYR* 3.5 6.3 - - - -
172D GLY 3.2 34.8 - - - -
173D PRO 3.1 21.3 - - - -
174D ARG 3.1 25.8 - - - +
175D GLU* 3.6 16.6 - - + -
177D HIS* 3.5 2.2 - - - -
178D LYS* 4.0 9.2 - - + -
214D VAL* 3.6 11.7 - - + -
400D NAP 3.0 42.9 + - - +
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Residues in contact with ILE 11 (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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10D PHE* 1.3 87.6 - - + +
12D GLY* 1.3 62.8 + - - +
14D ASN* 3.1 9.1 + - - +
15D ILE* 3.0 28.6 + - + +
75D GLU* 3.5 22.0 - - - +
167D TYR* 3.5 37.9 - - + +
170D VAL* 4.1 19.3 - - + -
214D VAL* 4.5 4.7 - - + -
217D VAL* 4.0 14.4 - - + -
218D ALA* 6.4 0.2 - - - -
400D NAP 2.8 46.9 + - + +
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Residues in contact with GLY 12 (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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4D VAL* 3.7 15.3 - - - +
6D GLY 3.5 18.5 + - - -
7D GLY* 3.8 6.7 - - - -
9D GLY 4.3 0.2 - - - -
10D PHE 3.3 0.4 - - - -
11D ILE* 1.3 79.6 - - - +
13D SER* 1.3 61.7 + - - +
15D ILE* 3.0 6.4 + - - +
16D VAL* 2.9 24.3 + - - +
75D GLU* 4.0 14.8 - - - +
400D NAP 4.3 0.8 + - - -
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Residues in contact with SER 13 (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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7D GLY 3.3 17.0 + - - -
9D GLY 2.7 25.0 + - - -
10D PHE 3.0 8.8 + - - -
12D GLY* 1.3 75.8 - - - +
14D ASN* 1.3 56.5 + - - +
16D VAL* 3.2 7.8 + - - +
17D LYS* 2.9 24.8 + - - +
41D ASN* 3.6 29.5 - - - +
42D LEU* 4.8 0.2 - - - -
45D LEU* 3.4 7.9 - - - +
174D ARG* 3.3 21.5 - - - +
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Residues in contact with ASN 14 (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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10D PHE* 2.8 22.4 + - - -
11D ILE* 3.1 9.7 + - + +
13D SER* 1.3 79.5 + - - +
15D ILE* 1.3 59.0 + - - +
17D LYS* 3.4 12.2 + - - +
18D ALA* 3.0 27.9 + - - +
173D PRO* 2.9 30.5 + - - +
174D ARG* 3.8 15.4 + - - +
214D VAL* 3.5 36.9 - - + +
215D GLY* 5.3 1.6 + - - -
218D ALA* 3.9 12.6 - - + +
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Residues in contact with ILE 15 (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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4D VAL* 4.4 5.8 - - + -
11D ILE* 3.0 20.9 + - + +
12D GLY* 3.0 7.6 + - - +
14D ASN* 1.3 75.2 - - - +
16D VAL* 1.3 63.2 + - - +
18D ALA* 3.2 6.7 + - - +
19D LEU* 2.9 36.7 + - + +
73D PHE* 4.0 28.9 - - + -
75D GLU* 3.6 31.4 - - + +
218D ALA* 4.7 8.1 - - - -
221D ASN* 3.5 39.3 - - + +
222D LEU* 4.5 6.5 - - + -
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Residues in contact with VAL 16 (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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4D VAL* 4.2 16.8 - - + -
7D GLY 4.2 8.3 - - - +
12D GLY 2.9 18.5 + - - +
13D SER 3.3 7.9 - - - +
15D ILE* 1.3 76.0 - - - +
17D LYS* 1.3 57.5 + - - +
19D LEU* 3.1 12.1 + - - +
20D ASN* 2.8 30.7 + - - +
27D ILE* 4.0 11.2 - - + -
29D VAL* 4.1 22.2 - - + -
42D LEU* 4.7 1.6 - - + -
45D LEU* 3.7 21.3 - - + -
47D ILE* 3.7 25.1 - - + -
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Residues in contact with LYS 17 (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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13D SER 2.9 14.3 + - - +
14D ASN* 3.7 16.6 - - - +
15D ILE 3.3 0.2 - - - -
16D VAL* 1.3 74.7 - - - +
18D ALA* 1.3 58.6 + - - +
20D ASN* 3.1 7.4 + - + +
21D ASP* 2.9 59.8 + - - -
45D LEU* 3.9 27.8 - - + +
174D ARG* 4.1 19.9 - - - +
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Residues in contact with ALA 18 (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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14D ASN 3.0 16.4 + - - +
15D ILE* 3.5 6.1 - - - +
16D VAL 3.2 0.2 - - - -
17D LYS* 1.3 79.0 - - - +
19D LEU* 1.3 61.3 + - - +
21D ASP* 3.2 11.6 + - - +
22D LYS* 3.1 17.8 + - - +
218D ALA* 4.0 20.0 - - + -
219D ASP* 5.4 4.5 - - - +
222D LEU* 3.8 27.5 - - + +
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Residues in contact with LEU 19 (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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2D ILE* 3.8 46.2 - - + -
4D VAL* 4.2 7.0 - - + -
15D ILE* 2.9 32.4 + - + +
16D VAL 3.4 5.8 - - - +
18D ALA* 1.3 71.6 - - - +
20D ASN* 1.3 67.3 + - - +
22D LYS* 3.0 9.4 + - + -
23D GLY 3.3 0.2 + - - -
24D ILE* 2.9 40.4 + - + +
27D ILE* 3.9 22.9 - - + -
73D PHE* 4.4 3.8 - - + -
222D LEU* 3.9 26.7 - - + -
225D LEU* 5.1 3.4 - - + -
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Residues in contact with ASN 20 (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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16D VAL* 2.8 16.5 + - - +
17D LYS* 3.3 12.1 - - + +
19D LEU* 1.3 76.0 - - - +
21D ASP* 1.3 57.2 + - - +
23D GLY* 2.7 26.3 + - - -
24D ILE 2.9 19.1 + - - +
25D THR* 3.8 7.9 - - + +
27D ILE* 3.8 4.4 - - - +
45D LEU* 3.6 15.6 - - + +
46D ASN* 2.8 56.4 + - - +
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Residues in contact with ASP 21 (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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17D LYS* 2.9 51.4 + - - +
18D ALA* 3.2 12.8 + - - +
20D ASN* 1.3 77.9 - - - +
22D LYS* 1.3 61.1 + - + +
23D GLY 3.2 1.0 + - - -
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Residues in contact with LYS 22 (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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18D ALA 3.1 13.2 + - - +
19D LEU* 3.0 11.3 + - - +
21D ASP* 1.3 78.9 - - + +
23D GLY* 1.3 59.9 + - - +
24D ILE* 3.3 16.3 + - + +
222D LEU* 3.8 24.2 - - + -
226D GLU* 3.1 30.3 + - - +
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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