Contacts of the strand formed by residues 30 - 37 (chain C) in PDB entry 5HJD
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 HIS 30 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17C ALA 4.6 5.2 - - - -
18C GLN 3.6 6.5 - - - +
19C VAL* 3.6 34.7 - - + +
20C ARG* 4.0 2.3 + - - +
28C PHE 3.9 5.2 - - - +
29C THR* 1.3 110.0 + - - +
31C ASP* 1.3 65.3 + - - +
32C TRP* 5.2 0.2 - - + -
76C SER* 3.3 9.4 - - - -
77C GLY 3.2 27.4 + - - +
78C TYR 4.9 3.6 + - - -
106C LEU* 3.8 44.4 - - + +
107C HIS 2.9 27.3 + - - -
108C LEU* 5.1 4.7 - - + -
109C GLU 5.7 0.2 - - - -
16D PRO* 5.5 9.4 - - + -
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Residues in contact with ASP 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C GLN* 2.8 48.7 + - - +
19C VAL 4.0 0.9 - - - +
20C ARG* 3.3 37.3 + - - +
30C HIS* 1.3 74.3 - - - +
32C TRP* 1.3 60.3 + - - +
75C GLU 3.4 7.0 - - - +
76C SER* 3.2 24.7 - - - +
77C GLY 4.5 0.2 - - - +
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Residues in contact with TRP 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C HIS* 5.4 0.2 - - + -
16C ARG 3.2 13.5 - - - +
17C ALA* 3.8 14.6 - - + -
30C HIS* 5.2 0.2 - - + -
31C ASP* 1.3 75.7 - - - +
33C MET* 1.3 69.7 + - - +
34C VAL* 3.6 19.3 - - + -
55C LEU* 3.5 24.5 - - + -
59C PHE* 3.9 19.4 - + - -
73C VAL* 3.3 22.4 - - + -
74C GLU* 3.5 2.1 - - - +
75C GLU* 2.5 61.4 + - + +
76C SER 4.4 1.0 - - - -
77C GLY* 4.1 23.6 - - - +
79C ALA 5.1 3.5 + - - -
81C PHE* 4.1 13.6 - + - -
83C LEU* 4.6 0.7 - - + -
104C LEU* 3.7 29.8 - - + +
106C LEU* 4.2 15.0 - - + -
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Residues in contact with MET 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C HIS* 3.1 3.1 - - - +
16C ARG* 2.7 74.1 + - + +
32C TRP* 1.3 78.7 - - - +
34C VAL* 1.3 62.9 + - - +
35C PHE* 3.5 30.1 - - + -
37C ARG* 6.3 0.4 - - - +
72C LYS* 3.7 46.7 - - - -
73C VAL 3.3 6.7 - - - +
74C GLU* 3.8 18.6 - - + +
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Residues in contact with VAL 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C GLY 3.6 11.4 - - - +
15C HIS* 3.9 7.9 - - + -
32C TRP* 3.6 19.5 - - + -
33C MET* 1.3 75.0 - - - +
35C PHE* 1.3 65.3 + - - +
53C PHE* 3.9 19.9 - - + -
55C LEU* 5.3 0.2 - - + -
72C LYS* 3.3 3.1 - - - +
73C VAL* 2.8 40.3 + - + +
83C LEU* 4.0 13.2 - - + -
85C ILE* 4.5 12.8 - - + -
102C TYR* 3.9 20.4 - - + -
104C LEU* 3.7 15.9 - - + -
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Residues in contact with PHE 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C GLU 4.3 2.9 - - - -
13C LEU* 3.7 1.0 - - - +
14C GLY 2.9 61.6 + - - +
15C HIS* 3.7 10.8 - - - -
16C ARG* 4.7 16.4 - - + -
33C MET* 3.5 33.4 - - + -
34C VAL* 1.3 80.2 - - - +
36C VAL* 1.3 68.6 + - - +
37C ARG* 3.7 52.7 - - + -
53C PHE* 4.2 3.1 - - - -
71C TYR 3.3 11.2 - - - +
72C LYS* 4.0 4.5 - - + -
85C ILE* 5.2 0.5 - - - +
115C ASN* 5.9 0.9 - - - -
116C HIS 4.7 0.9 - - - -
117C LEU* 3.7 26.5 - - + -
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Residues in contact with VAL 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C LEU* 4.4 23.6 - - + -
12C GLU 3.6 5.2 - - - +
13C LEU* 3.8 22.4 - - + -
35C PHE* 1.3 79.8 - - - +
37C ARG* 1.3 66.1 + - - +
44C ILE* 3.9 10.0 - - + +
51C VAL* 4.3 12.6 - - + -
53C PHE* 4.2 4.0 - - + -
71C TYR* 2.9 37.4 + - + +
85C ILE* 3.9 31.4 - - + -
87C VAL* 4.5 12.1 - - + -
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Residues in contact with ARG 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C LEU* 3.6 3.3 - - - +
12C GLU* 2.6 64.0 + - + +
16C ARG* 5.0 11.9 - - - +
33C MET* 6.3 0.4 - - - +
35C PHE* 3.7 39.6 - - + -
36C VAL* 1.3 75.6 - - - +
38C GLY* 1.3 70.9 + - - +
41C HIS* 5.8 6.3 + - - +
44C ILE* 4.0 11.9 - - - -
71C TYR* 5.4 0.9 - - + -
117C LEU* 4.0 17.4 - - - +
203C SO4 3.9 31.6 + - - +
115E ASN 4.9 4.2 + - - -
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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