Contacts of the helix formed by residues 51 - 72 (chain r) 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 GLY 51 (chain r).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50r ALA* 1.3 79.9 - - - +
52r ASP* 1.3 69.8 + - - +
53r THR 3.2 1.3 + - - -
54r VAL* 3.7 2.3 + - - +
55r GLN* 3.1 27.0 + - - +
88s TYR* 4.0 5.2 - - - -
91s LYS* 4.5 1.8 - - - +
117s GLU 3.4 10.3 + - - -
118s GLY* 3.2 32.7 - - - +
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Residues in contact with ASP 52 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49r GLU* 3.5 29.1 + - + +
50r ALA 3.4 0.4 - - - -
51r GLY* 1.3 79.5 - - - +
53r THR* 1.3 63.6 + - - +
55r GLN* 3.8 0.8 - - - +
56r PHE* 2.9 28.9 + - - +
97r PRO 3.8 7.2 - - - +
98r TYR* 4.0 11.6 - - + -
99r HIS* 3.2 31.1 + - - +
100r VAL* 3.7 3.4 - - + -
88s TYR* 2.5 37.9 + - - +
91s LYS* 3.4 13.9 - - - -
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Residues in contact with THR 53 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2r GLU* 4.9 4.3 - - - +
32r HIS* 6.2 0.2 - - - -
36r PHE* 5.2 2.0 - - - -
46r CYS* 3.9 14.7 - - - -
47r VAL* 3.5 15.0 - - - +
48r GLY* 3.3 27.4 - - - +
49r GLU 3.1 16.3 + - - +
50r ALA 3.4 13.9 + - - -
52r ASP* 1.3 76.7 - - - +
54r VAL* 1.3 71.3 + - - +
56r PHE* 3.9 0.2 - - - +
57r ALA* 2.9 31.3 + - - +
100r VAL* 3.6 12.1 - - + -
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Residues in contact with VAL 54 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32r HIS* 5.8 7.6 - - + +
36r PHE* 4.2 19.1 - - + -
50r ALA 5.5 1.6 - - - +
51r GLY 3.7 3.9 + - - +
53r THR* 1.3 86.2 + - - +
55r GLN* 1.3 71.2 + - + +
57r ALA* 4.3 4.5 - - - -
58r GLU* 2.9 51.5 + - + +
81s LYS* 4.6 7.0 - - + -
118s GLY 5.3 6.3 - - - +
120s ARG* 5.4 20.2 - - + +
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Residues in contact with GLN 55 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51r GLY* 3.1 19.5 + - - +
52r ASP 3.8 2.9 - - - +
54r VAL* 1.3 80.9 - - + +
56r PHE* 1.3 62.6 + - - +
58r GLU* 3.9 5.5 + - - +
59r TYR* 3.0 24.4 + - - +
98r TYR* 4.2 17.2 + - + +
84s ALA* 4.3 4.4 + - - +
85s ASN* 2.8 31.7 + - - +
88s TYR* 3.1 50.4 - - + +
118s GLY* 5.8 0.9 - - - +
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Residues in contact with PHE 56 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44r LEU* 5.2 2.2 - - + -
46r CYS* 4.7 3.4 - - - -
52r ASP 2.9 19.4 + - - +
53r THR 3.9 1.6 - - - +
55r GLN* 1.3 74.0 - - - +
57r ALA* 1.3 68.8 + - - +
59r TYR* 3.1 10.9 + + + +
60r ILE* 2.9 50.1 + - + +
84r THR* 3.5 23.8 - - - -
87r ASN* 4.5 4.7 - - + -
88r LEU* 3.8 31.4 - - + -
98r TYR* 4.0 31.5 - + + -
100r VAL* 3.8 23.1 - - + -
102r LEU* 3.9 26.9 - - + -
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Residues in contact with ALA 57 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36r PHE* 3.7 43.9 - - + -
44r LEU* 4.4 18.3 - - + +
46r CYS* 4.7 4.9 - - + -
53r THR 2.9 22.7 + - - +
54r VAL 3.9 1.3 - - - +
56r PHE* 1.3 75.7 - - - +
58r GLU* 1.3 57.1 + - - +
60r ILE* 3.3 2.3 + - - +
61r GLN* 2.9 31.0 + - - +
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Residues in contact with GLU 58 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96k LEU* 3.5 18.5 - - + +
99k GLU* 3.8 15.8 - - - +
36r PHE* 5.1 7.6 - - + -
54r VAL* 2.9 36.3 + - + +
55r GLN* 3.9 4.3 + - - +
57r ALA* 1.3 72.4 - - - +
59r TYR* 1.3 60.6 + - - +
61r GLN* 3.5 16.6 - - - +
62r LYS* 2.9 39.9 + - + +
81s LYS* 2.2 48.4 + - - +
85s ASN* 4.7 2.9 + - - +
120s ARG* 5.1 0.7 + - - -
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Residues in contact with TYR 59 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96k LEU* 4.7 10.7 - - + +
55r GLN 3.0 19.2 + - - +
56r PHE* 3.4 11.4 - + + +
58r GLU* 1.3 77.3 - - - +
60r ILE* 1.3 75.8 + - + +
62r LYS* 3.3 4.2 + - - +
63r ASN* 3.1 50.0 + - - -
83r PHE* 5.8 0.5 - - - -
87r ASN* 3.8 36.8 + - + -
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Residues in contact with ILE 60 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38r MET* 3.5 24.0 - - + -
44r LEU* 4.2 5.8 - - + -
56r PHE* 2.9 39.1 + - + +
57r ALA 3.6 6.5 - - - +
59r TYR* 1.3 92.5 - - + +
61r GLN* 1.3 64.2 + - - +
63r ASN* 3.2 4.7 + - - +
64r VAL* 2.9 30.6 + - + +
80r ALA* 6.3 0.2 - - - -
83r PHE* 4.1 9.3 - - + -
84r THR* 3.7 40.6 - - + -
87r ASN* 3.9 16.2 - - + +
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Residues in contact with GLN 61 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36r PHE* 4.3 19.7 - - + +
37r LYS* 2.9 31.4 + - - +
38r MET* 4.1 16.8 - - + -
57r ALA 2.9 17.8 + - - +
58r GLU* 3.5 13.1 - - - +
60r ILE* 1.3 77.7 - - - +
62r LYS* 1.3 88.6 + - - +
64r VAL* 3.2 4.6 + - - +
65r GLN* 2.9 35.6 + - + +
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Residues in contact with LYS 62 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92k GLN* 4.0 29.6 + - + +
95k ARG* 4.0 20.1 + - - +
96k LEU* 3.0 61.0 - - + +
99k GLU* 5.9 0.9 - - - -
58r GLU* 2.9 35.8 + - - +
59r TYR* 4.0 2.9 - - + +
61r GLN* 1.3 100.3 + - - +
63r ASN* 1.3 60.9 + - - +
65r GLN* 3.7 10.7 - - - +
66r LEU* 3.0 27.7 + - - +
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Residues in contact with ASN 63 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101j TYR* 5.4 2.6 + - - -
59r TYR* 3.1 60.6 + - - +
60r ILE 3.8 0.9 - - - +
61r GLN 3.2 0.2 - - - -
62r LYS* 1.3 76.6 - - - +
64r VAL* 1.3 58.5 + - - +
66r LEU* 3.3 17.8 - - - +
67r TYR* 3.0 26.0 + - - +
75r LEU* 5.8 0.2 - - - -
83r PHE* 3.5 35.7 - - + -
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Residues in contact with VAL 64 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38r MET* 3.3 52.0 - - + +
39r SER* 3.4 15.7 - - - +
42r ILE* 5.5 0.7 - - + -
60r ILE* 2.9 18.2 + - + +
61r GLN* 3.5 7.0 - - - +
63r ASN* 1.3 73.7 - - - +
65r GLN* 1.3 65.3 + - - +
67r TYR* 3.0 5.5 + - - +
68r LYS* 3.0 23.6 + - + +
75r LEU* 4.1 28.7 - - + -
80r ALA* 5.1 3.8 - - + -
83r PHE* 5.5 5.6 - - + -
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Residues in contact with GLN 65 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67k ASP* 4.3 10.6 - - - +
92k GLN* 3.3 28.9 + - - +
95k ARG* 5.9 2.0 - - - -
37r LYS 5.5 0.8 + - - -
38r MET* 3.2 27.9 + - - +
39r SER* 5.0 1.2 - - - +
40r GLU* 6.0 0.2 + - - -
61r GLN* 2.9 26.1 + - + +
62r LYS* 3.7 9.9 - - - +
64r VAL* 1.3 75.9 - - - +
66r LEU* 1.3 58.9 + - - +
68r LYS* 3.2 30.8 + - - +
69r MET* 2.9 40.6 + - - +
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Residues in contact with LEU 66 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88k ARG* 4.5 6.7 - - + +
89k VAL* 3.4 47.1 - - + +
92k GLN* 4.5 10.5 - - + +
62r LYS 3.0 14.5 + - - +
63r ASN* 3.3 22.9 - - - +
65r GLN* 1.3 76.3 - - - +
67r TYR* 1.3 66.9 + - - +
69r MET* 3.3 2.8 + - + -
70r ARG* 2.9 55.7 + - + +
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Residues in contact with TYR 67 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97j TYR* 2.5 33.9 + + - -
101j TYR* 3.8 23.1 - + - +
103j GLU* 5.4 0.3 + - - -
109j GLN* 2.8 20.4 + - - -
142j HIS* 5.5 0.2 + - - -
63r ASN 3.0 13.7 + - - +
64r VAL 3.0 9.6 + - - +
66r LEU* 1.3 78.3 - - - +
68r LYS* 1.3 58.7 + - - +
70r ARG* 3.1 4.2 + - - +
71r ASN* 2.9 53.3 + - + +
73r TYR* 4.0 32.0 - + - -
75r LEU* 3.6 41.9 - - + +
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Residues in contact with LYS 68 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67k ASP* 4.3 20.4 + - - -
38r MET 5.6 1.1 - - - +
39r SER* 5.4 3.7 - - - +
40r GLU* 4.1 17.0 + - - +
64r VAL* 3.0 12.5 + - + +
65r GLN* 3.5 34.0 + - - +
67r TYR* 1.3 80.5 - - - +
69r MET* 1.4 60.2 + - - +
72r GLY* 3.0 29.4 + - - -
73r TYR 3.9 13.7 - - - +
74r GLU* 3.8 39.8 + - + +
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Residues in contact with MET 69 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64k ALA* 4.4 15.6 - - + +
65k LEU 3.8 13.5 - - - +
66k ASP* 3.5 29.2 - - - +
67k ASP* 3.1 31.6 - - - +
88k ARG* 3.4 35.1 + - + -
92k GLN* 3.9 24.9 - - + +
65r GLN* 2.9 27.1 + - - +
66r LEU* 3.8 4.3 - - - +
68r LYS* 1.4 82.7 - - - +
70r ARG* 1.3 61.1 + - - +
71r ASN 3.8 0.2 + - - -
72r GLY* 4.7 1.4 + - - -
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Residues in contact with ARG 70 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116j ASP* 5.0 4.8 + - - -
85k ASN* 3.4 45.9 + - - +
88k ARG* 4.1 19.1 + - + +
89k VAL* 3.8 24.7 - - - +
66r LEU* 2.9 45.6 + - + +
67r TYR* 4.0 3.4 - - - +
69r MET* 1.3 79.4 - - - +
71r ASN* 1.3 73.9 + - - +
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Residues in contact with ASN 71 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108j GLU* 5.3 3.6 - - - +
109j GLN* 3.3 46.5 + - + +
112j THR* 5.7 0.3 + - - -
143j TYR* 4.5 2.8 + - - -
67r TYR* 2.9 45.1 + - + +
70r ARG* 1.3 94.1 + - - +
72r GLY* 1.3 58.8 + - - +
73r TYR* 3.3 31.6 + - + +
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Residues in contact with GLY 72 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143j TYR* 5.2 2.5 - - - -
68r LYS* 3.0 18.6 + - - +
69r MET 4.7 1.3 + - - -
70r ARG 3.8 0.6 - - - -
71r ASN* 1.3 77.2 - - - +
73r TYR* 1.3 59.9 + - - +
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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
------------------------------------------------------------
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