Contacts of the strand formed by residues 5 - 19 (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 CYS 5 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A CYS* 2.0 47.6 - - - -
6A ALA 4.0 1.8 - - - -
7A VAL* 4.1 4.9 - - + -
132A ARG* 3.8 34.3 - - - +
136A LEU* 4.0 7.5 - - + +
4C SER* 1.3 75.0 + - - +
6C ALA* 1.3 58.5 + - - +
7C VAL* 3.7 15.5 - - - -
124C PHE 3.6 1.2 - - - +
125C ASN* 3.6 2.1 - - - +
126C ASN* 2.7 42.1 + - - +
127C PRO* 3.9 3.8 - - + +
132C ARG* 4.2 0.4 - - - -
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Residues in contact with ALA 6 (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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4A SER 3.4 3.8 - - - +
5A CYS* 3.4 2.1 - - - -
6A ALA* 3.2 38.5 + - + +
4C SER* 5.4 4.0 - - - +
5C CYS* 1.3 72.8 - - - +
7C VAL* 1.3 62.8 + - - +
8C GLN* 3.9 8.3 + - + +
123C THR* 5.7 4.3 - - - -
124C PHE 3.6 5.4 - - - -
125C ASN* 4.0 15.3 - - - +
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Residues in contact with VAL 7 (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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4A SER 3.6 6.1 - - - +
5A CYS* 4.0 5.6 - - + -
5C CYS* 3.7 20.4 - - - -
6C ALA* 1.3 72.3 - - - +
8C GLN* 1.3 67.5 + - - +
9C VAL* 4.3 0.7 - - + -
122C LEU 3.5 1.0 - - - +
123C THR* 3.3 2.4 - - - -
124C PHE* 2.7 45.0 + - + +
127C PRO* 3.6 28.7 - - + -
132C ARG* 3.9 12.1 - - + -
135C LEU* 3.9 35.4 - - + -
136C LEU* 4.5 13.9 - - + -
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Residues in contact with GLN 8 (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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3A SER* 3.2 27.2 - - - -
4A SER* 3.0 30.2 + - - +
6C ALA* 4.5 8.1 - - + +
7C VAL* 1.3 77.5 - - - +
9C VAL* 1.3 63.1 + - - +
10C LYS* 5.9 2.7 - - + -
121C LYS* 3.9 25.8 + - + +
122C LEU 3.2 4.9 - - - +
123C THR* 3.9 27.3 - - + +
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Residues in contact with VAL 9 (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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2A ALA 4.2 5.6 - - - +
3A SER* 4.1 5.4 - - - -
7C VAL* 4.3 0.9 + - + -
8C GLN* 1.3 79.3 - - - +
10C LYS* 1.3 65.6 + - - +
11C LEU* 4.2 0.4 + - + -
47C PHE* 3.9 38.1 - - + -
121C LYS* 3.8 2.9 - - - +
122C LEU* 2.9 50.8 + - + +
124C PHE* 4.0 10.3 - - + -
135C LEU* 3.6 41.7 - - + +
138C ALA* 5.2 1.3 - - + -
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Residues in contact with LYS 10 (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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2A ALA* 3.6 41.5 + - + +
3A SER* 5.2 0.9 - - - +
8C GLN* 5.9 2.0 - - + -
9C VAL* 1.3 78.4 - - - +
11C LEU* 1.3 71.3 + - - +
38C GLY* 4.1 2.1 - - - -
39C PRO* 3.2 31.4 - - + +
40C GLU* 5.3 1.2 + - - -
42C SER* 5.3 0.3 + - - -
44C ILE* 4.9 2.3 - - - +
47C PHE* 5.5 0.3 - - - -
120C GLU 3.7 4.0 - - - +
121C LYS* 4.6 26.5 - - + +
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Residues in contact with LEU 11 (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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9C VAL* 5.4 0.9 - - + +
10C LYS* 1.3 84.3 - - - +
12C GLU* 1.3 61.1 + - - +
13C LEU* 4.0 11.4 - - + -
36C VAL* 4.4 8.3 - - + -
37C ARG 3.8 8.3 - - - +
39C PRO* 4.2 5.2 - - - +
44C ILE* 3.9 33.2 - - + -
47C PHE* 4.1 13.7 - - + -
48C VAL* 5.4 0.2 - - + -
87C VAL* 4.3 29.6 - - + -
100C PHE* 4.6 9.0 - - + -
118C ARG 3.9 0.7 - - - +
119C CYS* 3.9 2.9 - - - +
120C GLU* 2.8 38.9 + - + +
122C LEU* 3.8 29.4 - - + -
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Residues in contact with GLU 12 (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* 1.3 73.4 - - - +
13C LEU* 1.3 63.9 + - - +
14C GLY 4.1 0.3 + - - -
35C PHE* 4.0 1.6 - - - +
36C VAL* 3.6 2.6 - - - -
37C ARG* 2.6 66.4 + - - +
39C PRO* 3.9 26.7 - - + +
117C LEU* 3.5 42.0 - - + +
118C ARG 3.6 9.0 - - - +
119C CYS* 5.2 5.3 - - - -
117E LEU* 3.9 21.3 + - - +
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Residues in contact with LEU 13 (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* 4.1 12.8 - - + -
12C GLU* 1.3 77.1 - - - +
14C GLY* 1.3 56.9 + - - +
35C PHE 3.7 4.5 - - - +
36C VAL* 3.8 21.1 - - + -
85C ILE* 4.1 19.3 - - + -
100C PHE* 3.8 41.7 - - + -
102C TYR* 3.9 21.1 - - + -
117C LEU* 3.5 2.3 - - - +
118C ARG* 2.6 55.0 + - + +
120C GLU* 3.9 25.1 - - + -
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Residues in contact with GLY 14 (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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13C LEU* 1.3 75.0 - - - +
15C HIS* 1.3 60.3 + - - +
34C VAL* 3.6 2.9 - - - +
35C PHE* 2.9 53.0 + - - +
102C TYR* 3.1 16.0 + - - -
116C HIS 3.2 12.8 - - - -
117C LEU* 4.1 0.9 - - - -
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Residues in contact with HIS 15 (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* 1.3 75.3 - - - +
16C ARG* 1.3 64.0 + - - +
17C ALA* 4.3 9.0 - - + -
32C TRP* 5.4 0.2 - - + -
33C MET 3.1 13.7 - - - +
34C VAL* 3.9 7.9 - - + -
35C PHE* 3.7 4.6 - - - -
102C TYR* 2.6 37.8 + + + +
103C ASP 3.9 5.4 - - - -
104C LEU* 3.9 19.7 - - + -
105C PHE* 3.0 60.4 + + - -
114C VAL* 3.3 19.6 - - + +
115C ASN* 4.0 0.9 - - - -
116C HIS* 3.2 32.3 + - + +
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Residues in contact with ARG 16 (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* 1.3 75.1 - - - +
17C ALA* 1.3 60.9 + - - +
18C GLN* 4.0 3.1 - - + +
32C TRP* 3.2 4.2 - - - +
33C MET* 2.7 69.6 + - + +
35C PHE* 4.7 12.4 - - + -
37C ARG* 5.0 15.6 - - - +
114C VAL 3.3 9.4 - - - +
115C ASN* 3.2 34.5 + - - +
112E PRO* 6.3 1.0 - - - +
115E ASN* 5.7 4.0 - - - +
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Residues in contact with ALA 17 (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* 4.3 4.0 - - + -
16C ARG* 1.3 74.0 - - - +
18C GLN* 1.3 62.6 + - - +
19C VAL 3.8 1.7 + - - -
30C HIS* 4.6 4.5 - - - -
31C ASP 4.9 0.2 - - - -
32C TRP* 3.8 10.1 - - + -
105C PHE 3.9 6.1 - - - +
106C LEU* 3.5 30.5 - - + -
107C HIS 5.5 0.3 + - - -
113C PRO* 4.5 3.2 - - - +
114C VAL* 3.4 49.5 + - + +
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Residues in contact with GLN 18 (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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16C ARG* 4.0 3.9 - - + +
17C ALA* 1.3 73.7 - - - +
19C VAL* 1.3 92.1 + - - +
20C ARG* 6.3 0.2 - - + -
30C HIS* 3.6 2.7 - - - +
31C ASP* 2.8 52.6 + - - +
113C PRO* 4.3 22.3 - - + +
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Residues in contact with VAL 19 (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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17C ALA 3.8 2.8 + - - -
18C GLN* 1.3 101.2 + - - +
20C ARG* 1.3 64.8 + - - +
21C LYS* 3.7 26.7 + - + +
29C THR* 4.1 1.3 - - - +
30C HIS* 3.6 31.6 - - + +
107C HIS 5.1 2.0 - - - +
108C LEU 5.6 0.7 - - - +
109C GLU* 4.7 27.4 - - + +
113C PRO* 6.0 0.6 - - + +
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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