Contacts of the helix formed by residues 30 - 41 (chain P) in PDB entry 5GSE
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 30 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164I A 3.1 35.4 - - - +
165I A 3.1 16.1 + - - -
62O ILE* 5.9 0.2 - - + -
63O ARG* 5.2 11.4 - - + +
66O PRO* 6.1 0.7 - - + -
27P GLN 4.3 5.4 - - - -
28P GLY 2.8 13.0 + - - +
29P ILE* 1.3 76.0 - - - +
31P LYS* 1.3 65.9 + - - +
32P PRO* 2.9 16.6 - - - +
33P ALA* 3.3 27.0 + - + +
34P ILE* 3.2 19.4 + - - +
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Residues in contact with LYS 31 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165I A 4.1 6.4 + - - +
82J C 5.7 1.2 + - - -
29P ILE 3.7 0.8 + - - -
30P THR* 1.3 73.7 + - - +
32P PRO* 1.3 72.8 - - + +
34P ILE* 3.3 4.9 + - - +
35P ARG* 2.9 32.0 + - - +
51P TYR* 3.5 53.2 + - + -
55P ARG* 4.1 19.7 - - - +
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Residues in contact with PRO 32 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164I A 3.8 37.5 - - + +
165I A 4.0 7.6 - - + +
30P THR* 2.9 21.8 - - - +
31P LYS* 1.3 90.5 - - + +
33P ALA* 1.3 57.0 + - - +
35P ARG* 3.2 10.8 + - + +
36P ARG* 2.8 43.0 + - - +
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Residues in contact with ALA 33 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61O LEU 3.6 15.3 - - - +
62O ILE* 3.6 23.1 - - + -
29P ILE* 4.9 2.0 - - + -
30P THR* 3.3 31.0 + - + +
31P LYS 3.2 0.6 - - - -
32P PRO* 1.3 76.8 - - - +
34P ILE* 1.3 63.9 + - - +
36P ARG* 3.0 19.5 + - - +
37P LEU* 2.9 26.8 + - - +
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Residues in contact with ILE 34 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100O LEU* 5.9 0.9 - - + -
104O PHE* 3.7 23.2 - - + -
29P ILE* 3.7 33.2 - - + +
30P THR 3.2 7.0 + - - +
31P LYS* 3.3 6.0 + - - +
33P ALA* 1.3 75.3 - - - +
35P ARG* 1.3 64.0 + - - +
37P LEU* 3.2 14.3 + - + +
38P ALA* 2.9 22.2 + - + +
46P ILE* 6.0 0.4 - - + -
50P ILE* 5.0 1.1 - - + -
51P TYR* 3.5 42.6 - - + +
54P THR* 4.0 21.5 - - + +
55P ARG* 3.8 16.2 - - + +
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Residues in contact with ARG 35 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82J C 2.4 63.9 + - - +
83J G 4.3 2.6 + - - -
50O GLU* 5.1 5.1 + - - +
31P LYS* 2.9 25.1 + - - +
32P PRO* 3.3 14.6 - - + +
34P ILE* 1.3 76.7 - - - +
36P ARG* 1.3 57.6 + - + +
38P ALA* 3.2 5.2 + - - +
39P ARG* 2.9 63.6 + - + +
46P ILE* 3.5 23.6 - - + +
51P TYR* 2.5 36.1 + - + -
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Residues in contact with ARG 36 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163I A 4.5 0.2 - - - -
164I A 2.2 45.3 + - - -
50O GLU* 6.0 0.9 - - - +
54O TYR* 3.1 46.4 + - + +
61O LEU* 2.2 59.4 + - + +
62O ILE* 4.5 0.2 - - - +
63O ARG* 3.7 21.2 - - - +
32P PRO* 2.8 27.1 + - - +
33P ALA* 3.2 21.8 - - - +
35P ARG* 1.3 73.4 - - + +
37P LEU* 1.3 66.8 + - - +
39P ARG* 2.8 21.6 + - + +
40P ARG 2.9 11.8 + - - -
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Residues in contact with LEU 37 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61O LEU* 3.9 17.3 - - + -
62O ILE* 3.8 20.2 - - + -
97O GLU* 3.8 31.4 - - + +
100O LEU* 3.6 33.0 - - + -
101O VAL* 3.9 27.0 - - + +
104O PHE* 3.8 15.5 - - + -
29P ILE* 5.9 0.7 - - + -
33P ALA 2.9 15.0 + - - +
34P ILE* 3.4 16.4 - - + +
36P ARG* 1.3 74.5 - - - +
38P ALA* 1.3 63.1 + - - +
40P ARG* 3.4 3.3 + - - +
41P GLY* 3.0 19.1 + - - -
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Residues in contact with ALA 38 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104O PHE* 3.6 36.4 - - + -
34P ILE 2.9 13.5 + - - +
35P ARG* 3.4 10.5 - - - +
36P ARG 3.2 0.2 - - - -
37P LEU* 1.3 75.8 - - - +
39P ARG* 1.3 61.1 + - + +
41P GLY 3.1 2.3 + - - -
42P GLY 3.1 5.5 + - - -
43P VAL* 2.9 38.7 + - + +
46P ILE* 4.2 15.7 - - + -
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Residues in contact with ARG 39 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82J C 4.0 2.0 + - - -
83J G 4.2 4.6 + - - -
47O ALA* 3.2 40.4 + - - +
50O GLU* 3.3 39.0 + - + +
51O ILE* 3.4 24.7 - - + +
54O TYR* 4.2 5.4 - - + -
35P ARG* 2.9 63.8 + - - +
36P ARG* 2.8 17.6 + - - +
38P ALA* 1.3 71.9 - - - +
40P ARG* 1.3 57.4 + - - +
42P GLY 3.0 14.0 + - - -
43P VAL 3.2 12.8 + - - -
44P LYS* 2.3 40.6 + - - +
46P ILE* 5.1 5.1 - - - +
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Residues in contact with ARG 40 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106M GLY* 5.1 9.1 - - - -
107M VAL* 3.7 31.3 - - + +
54O TYR* 2.8 26.1 + - + +
55O GLN* 3.2 26.9 + - - +
57O SER* 2.4 33.8 + - - -
58O THR* 3.2 21.5 + - - +
59O GLU 3.0 29.7 + - - -
60O LEU* 6.1 0.2 - - - +
61O LEU* 3.8 24.3 - - + +
97O GLU* 4.4 7.3 + - - +
101O VAL* 4.4 18.8 - - + +
36P ARG 2.9 10.9 + - - +
37P LEU 3.7 7.4 - - - +
39P ARG* 1.3 75.9 - - - +
41P GLY* 1.3 57.6 + - - +
42P GLY 3.2 4.5 + - - -
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Residues in contact with GLY 41 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107M VAL* 5.8 0.4 - - - -
55O GLN* 4.4 1.6 - - - -
101O VAL* 4.0 22.3 - - - +
104O PHE* 4.2 2.9 - - - +
105O GLU* 3.4 33.9 + - - +
108O ASN* 4.5 3.3 + - - +
37P LEU 3.0 14.9 + - - -
38P ALA 3.1 7.1 + - - -
40P ARG* 1.3 74.3 - - - +
42P GLY* 1.3 59.2 + - - +
43P VAL* 3.5 1.9 + - - +
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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
------------------------------------------------------------
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