Contacts of the helix formed by residues 20 - 32 (chain n) in PDB entry 5GJQ
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 VAL 20 (chain n).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83h MET* 4.6 12.4 - - + +
132h ARG* 4.1 20.2 - - - +
10n SER 4.7 0.2 - - - +
11n ALA* 4.0 30.3 - - + +
13n THR 4.2 8.3 - - - +
14n PHE* 3.7 25.8 - - + -
19n ARG* 1.3 79.4 - - - +
21n PHE* 1.3 64.1 + - - +
22n GLN 4.2 4.5 - - - +
23n VAL* 3.3 36.7 + - + +
24n GLU* 3.5 13.2 + - - +
123n THR 4.8 2.0 - - - +
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Residues in contact with PHE 21 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3n ILE* 3.5 48.2 - - + -
7n TYR 3.9 10.0 + - - +
8n ASP* 3.7 21.7 - - + +
10n SER 5.7 0.4 + - - -
13n THR 4.8 3.0 + - - -
15n SER* 3.5 31.4 - - - -
17n ASP* 6.1 0.4 - - + -
19n ARG* 3.3 46.9 + - - -
20n VAL* 1.3 70.2 - - - +
22n GLN* 1.3 60.6 + - - +
24n GLU* 3.2 16.1 + - - +
25n TYR* 2.9 57.5 + + + -
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Residues in contact with GLN 22 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11m THR 4.3 4.0 - - - +
12m VAL* 3.8 5.2 - - - +
13m TRP* 2.8 58.5 + - - +
8n ASP* 2.8 27.5 + - - +
9n LEU* 3.3 16.7 + - - +
10n SER* 3.5 28.2 + - - +
11n ALA* 3.9 20.2 - - + +
20n VAL* 3.2 2.1 - - + +
21n PHE* 1.3 77.8 - - - +
23n VAL* 1.3 57.9 + - - +
25n TYR* 3.2 5.2 + - - +
26n ALA* 2.9 28.9 + - - +
130n PRO* 4.6 9.5 - - + +
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Residues in contact with VAL 23 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20n VAL* 3.3 29.3 + - + +
21n PHE 3.2 0.4 - - - -
22n GLN* 1.3 77.5 - - - +
24n GLU* 1.3 59.7 + - + +
26n ALA* 3.3 6.6 + - - +
27n MET* 2.9 35.6 + - + +
123n THR* 3.9 29.2 - - + -
130n PRO* 4.1 9.2 - - + -
153n PRO* 4.2 6.1 - - + +
154n SER* 3.7 37.9 - - - +
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Residues in contact with GLU 24 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19n ARG* 2.6 55.4 + - - +
20n VAL 3.6 12.6 - - - +
21n PHE* 3.2 24.1 + - - +
23n VAL* 1.3 79.4 - - + +
25n TYR* 1.3 62.4 + - + +
27n MET* 3.4 15.7 + - - +
28n LYS* 3.0 31.6 + - - +
31n GLU* 4.8 0.9 - - - +
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Residues in contact with TYR 25 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6m TYR* 4.2 1.6 - + - -
13m TRP* 3.9 19.0 - - + -
14m SER 3.3 16.6 - - - +
15m PRO* 3.5 44.2 - - + +
17m GLY* 3.5 9.2 - - - -
3n ILE 4.2 6.8 + - - -
4n GLY* 5.0 0.3 - - - -
8n ASP* 2.7 48.7 + - + +
21n PHE* 2.9 49.2 + + + +
22n GLN* 3.2 7.8 + - - +
24n GLU* 1.3 79.6 - - + +
26n ALA* 1.3 66.8 + - - +
28n LYS* 3.0 16.2 + - - +
29n ALA 3.0 16.3 + - - -
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Residues in contact with ALA 26 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13m TRP* 3.6 40.5 - - + +
22n GLN 2.9 11.3 + - - +
23n VAL* 3.5 9.0 - - - +
25n TYR* 1.3 75.4 - - - +
27n MET* 1.3 65.7 + - - +
29n ALA* 2.9 15.2 + - - +
30n VAL* 3.0 15.2 + - - +
130n PRO* 4.3 10.5 - - + -
131n PHE 4.1 13.7 - - - +
132n GLY* 4.2 1.7 - - - -
153n PRO* 4.4 3.8 - - + -
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Residues in contact with MET 27 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23n VAL* 2.9 21.6 + - + +
24n GLU* 3.4 18.2 - - - +
26n ALA* 1.3 77.0 - - - +
28n LYS* 1.3 57.3 + - - +
30n VAL* 2.9 25.1 + - + +
31n GLU* 2.9 23.1 + - - +
152n ASP* 4.0 18.6 - - + +
153n PRO* 4.0 16.4 - - + -
154n SER* 3.9 32.5 - - - +
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Residues in contact with LYS 28 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15m PRO 3.5 21.0 + - - +
16m GLN* 4.1 17.0 - - - +
17m GLY* 4.1 4.7 - - - +
24n GLU* 3.0 17.9 + - - +
25n TYR* 3.2 19.9 - - - +
26n ALA 3.0 0.2 - - - -
27n MET* 1.3 73.9 - - - +
29n ALA* 1.3 62.5 + - - +
31n GLU* 3.2 32.5 + - + +
32n ASN* 3.1 30.8 - - - +
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Residues in contact with ALA 29 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13m TRP* 3.2 37.9 - - + -
17m GLY* 3.4 16.5 - - - +
25n TYR 3.0 5.5 + - - -
26n ALA 2.9 13.1 + - - +
28n LYS* 1.3 77.1 - - - +
30n VAL* 1.3 60.7 + - - +
32n ASN* 3.5 12.9 + - - +
33n SER* 3.9 5.4 + - - -
79n GLY* 4.3 10.2 - - - -
80n LEU* 5.5 3.6 - - + +
132n GLY* 4.6 5.2 - - - +
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Residues in contact with VAL 30 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26n ALA 3.0 12.1 + - - +
27n MET* 2.9 10.4 + - + +
29n ALA* 1.3 74.7 - - - +
31n GLU* 1.3 67.4 + - + +
33n SER* 3.0 18.5 + - - -
78n ALA* 3.9 13.9 - - + +
79n GLY* 4.5 4.7 - - - -
132n GLY 3.9 1.1 - - - -
133n CYS* 3.6 35.0 - - - +
134n SER* 3.5 24.9 - - - +
153n PRO* 3.8 13.2 - - + -
165n ILE* 5.3 1.6 - - + -
166n GLY* 3.8 12.8 - - - +
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Residues in contact with GLU 31 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379L LYS* 4.3 19.4 + - - +
24n GLU 4.8 0.7 - - - +
27n MET* 2.9 16.8 + - - +
28n LYS* 3.2 44.5 + - + +
30n VAL* 1.3 78.2 - - + +
32n ASN* 1.3 60.7 + - - +
33n SER 3.1 4.4 + - - -
166n GLY 4.7 7.6 - - - +
167n LYS* 3.3 27.9 + - - +
169n ARG* 6.4 0.4 - - - +
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Residues in contact with ASN 32 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16m GLN 3.7 21.4 + - - -
17m GLY 4.9 5.2 + - - +
18m ARG* 5.4 5.5 - - - +
28n LYS* 3.1 20.5 + - - +
29n ALA* 3.9 8.3 - - - +
30n VAL 3.1 1.0 - - - -
31n GLU* 1.3 80.1 - - - +
33n SER* 1.3 57.0 + - - +
167n LYS* 3.2 25.0 + - - +
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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