Contacts of the helix formed by residues 9 - 22 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6M GLY 2.7 14.9 + - - -
8M ALA* 1.3 81.4 - - - +
10M PHE* 1.3 58.4 + - - -
11M ILE 3.7 1.3 - - - -
13M SER* 2.7 34.5 + - - -
31M ASP* 3.2 4.1 + - - -
38M LYS* 4.9 0.2 - - - -
41M ASN* 4.2 0.7 - - - -
177M HIS* 3.8 9.6 - - - -
400M NAP 3.5 22.7 - - - -
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Residues in contact with PHE 10 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9M GLY* 1.3 70.6 - - - -
11M ILE* 1.3 71.2 + - + +
13M SER* 3.0 9.4 + - - -
14M ASN* 2.8 28.1 + - - -
170M VAL* 3.6 32.1 - - + -
171M TYR* 3.5 5.4 - - - -
172M GLY 3.2 34.3 - - - -
173M PRO 3.1 21.8 - - - -
174M ARG 3.1 25.4 - - - +
175M GLU* 3.6 15.7 - - + -
177M HIS* 3.5 2.4 - - + -
178M LYS* 4.0 9.4 - - + -
214M VAL* 3.6 12.1 - - + -
400M NAP 2.9 40.6 + - - +
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Residues in contact with ILE 11 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10M PHE* 1.3 86.4 - - + +
12M GLY* 1.3 62.2 + - - +
14M ASN* 3.1 10.0 + - + +
15M ILE* 3.0 28.0 + - + +
75M GLU* 3.5 21.3 - - - +
167M TYR* 3.5 38.1 - - + +
170M VAL* 4.1 18.8 - - + -
214M VAL* 4.5 4.7 - - + -
217M VAL* 4.1 14.6 - - + -
400M NAP 2.7 49.8 + - + +
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Residues in contact with GLY 12 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4M VAL* 3.7 16.0 - - - +
6M GLY 3.5 19.0 + - - -
7M GLY* 3.8 7.0 - - - -
10M PHE 3.3 0.4 - - - -
11M ILE* 1.3 78.8 - - - +
13M SER* 1.3 62.0 + - - +
15M ILE* 3.0 6.1 + - - +
16M VAL* 2.9 23.9 + - - +
75M GLU* 4.0 15.0 - - - +
400M NAP 4.3 1.0 + - - -
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Residues in contact with SER 13 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7M GLY 3.3 17.9 + - - -
9M GLY 2.7 25.1 + - - -
10M PHE 3.0 8.3 + - - -
12M GLY* 1.3 75.3 - - - +
14M ASN* 1.3 57.7 + - - +
16M VAL* 3.2 8.8 + - - +
17M LYS* 2.9 24.6 + - - +
41M ASN* 3.6 29.2 - - - +
45M LEU* 3.4 7.9 - - - +
174M ARG* 3.3 21.4 - - - +
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Residues in contact with ASN 14 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10M PHE* 2.8 22.6 + - - -
11M ILE 3.1 8.8 + - - +
13M SER* 1.3 80.1 + - - +
15M ILE* 1.3 59.6 + - - +
17M LYS* 3.4 11.9 + - - +
18M ALA* 3.0 28.1 + - - +
173M PRO* 2.9 29.5 + - - +
174M ARG* 3.8 15.1 + - - +
214M VAL* 3.5 37.7 - - + +
215M GLY* 5.3 1.8 + - - -
218M ALA* 3.9 12.5 - - + +
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Residues in contact with ILE 15 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4M VAL* 4.4 5.6 - - + -
11M ILE* 3.0 19.6 + - + +
12M GLY* 3.0 7.8 + - - +
14M ASN* 1.3 75.1 - - - +
16M VAL* 1.3 67.2 + - - +
18M ALA* 3.2 7.4 + - - +
19M LEU* 2.9 37.3 + - + +
73M PHE* 4.0 27.8 - - + -
75M GLU* 3.6 32.5 - - + +
218M ALA* 4.7 9.6 - - - -
221M ASN* 3.5 38.6 - - + +
222M LEU* 4.5 6.3 - - + -
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Residues in contact with VAL 16 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4M VAL* 4.2 17.0 - - + -
7M GLY 4.1 9.0 - - - +
12M GLY 2.9 17.8 + - - +
13M SER 3.3 7.9 - - - +
15M ILE* 1.3 76.6 - - - +
17M LYS* 1.3 57.6 + - - +
19M LEU* 3.1 11.0 + - - +
20M ASN* 2.8 30.8 + - - +
27M ILE* 4.0 11.2 - - + -
29M VAL* 4.1 22.2 - - + -
42M LEU* 4.7 1.3 - - + -
45M LEU* 3.7 21.5 - - + -
47M ILE* 3.8 25.6 - - + -
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Residues in contact with LYS 17 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13M SER 2.9 13.9 + - - +
14M ASN* 3.7 15.9 - - - +
15M ILE 3.3 0.2 - - - -
16M VAL* 1.3 76.3 - - - +
18M ALA* 1.3 57.9 - - - +
20M ASN* 3.1 7.3 + - + +
21M ASP* 2.9 60.4 + - - +
45M LEU* 3.9 27.6 - - + -
174M ARG* 4.1 20.2 - - - +
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Residues in contact with ALA 18 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14M ASN 3.0 17.2 + - - +
15M ILE* 3.5 5.6 - - - +
16M VAL 3.2 0.2 - - - -
17M LYS* 1.3 78.6 - - - +
19M LEU* 1.3 61.8 + - - +
21M ASP* 3.2 13.0 + - - +
22M LYS* 3.1 18.4 + - - +
218M ALA* 4.0 20.0 - - + +
219M ASP* 5.3 4.7 - - - +
222M LEU* 3.8 27.4 - - + +
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Residues in contact with LEU 19 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2M ILE* 3.8 46.2 - - + -
4M VAL* 4.2 7.4 - - + -
15M ILE* 2.9 32.2 + - + +
16M VAL* 3.4 6.1 - - - +
18M ALA* 1.3 72.0 - - - +
20M ASN* 1.3 67.0 + - - +
22M LYS* 3.0 10.7 + - + +
23M GLY 3.3 0.2 + - - -
24M ILE* 2.9 40.2 + - + +
27M ILE* 3.9 21.3 - - + -
73M PHE* 4.4 4.3 - - + -
222M LEU* 3.9 26.2 - - + -
225M LEU* 4.9 3.8 - - + -
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Residues in contact with ASN 20 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16M VAL* 2.8 18.1 + - - +
17M LYS* 3.3 11.7 - - + +
19M LEU* 1.3 75.7 - - - +
21M ASP* 1.3 57.0 + - - +
23M GLY* 2.7 26.3 + - - -
24M ILE 2.9 19.0 + - - -
25M THR* 3.8 9.1 - - + +
27M ILE* 3.8 4.2 - - - +
45M LEU* 3.6 15.7 - - + +
46M ASN* 2.8 54.6 + - - +
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Residues in contact with ASP 21 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17M LYS* 2.9 51.3 + - - +
18M ALA* 3.2 12.7 + - - +
20M ASN* 1.3 78.8 - - - +
22M LYS* 1.3 61.5 + - + +
23M GLY 3.2 0.7 + - - -
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Residues in contact with LYS 22 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18M ALA 3.1 11.2 + - - +
19M LEU* 3.0 12.0 + - + +
21M ASP* 1.3 78.1 - - + +
23M GLY* 1.3 60.4 + - - +
24M ILE* 3.3 16.1 + - + +
222M LEU* 3.8 24.0 - - + -
226M GLU* 3.1 30.6 + - - +
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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