Contacts of the strand formed by residues 114 - 125 (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 VAL 114 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15C HIS* 3.3 41.3 - - + +
16C ARG* 3.3 21.5 - - - +
17C ALA* 3.4 35.7 + - + +
105C PHE* 3.7 12.6 - - + +
107C HIS* 3.1 40.2 - - + +
113C PRO* 1.3 75.2 - - + +
115C ASN* 1.3 64.1 + - - +
116C HIS* 4.1 6.7 - - + +
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Residues in contact with ASN 115 (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 4.0 1.3 - - - +
16C ARG* 3.2 35.6 + - - +
35C PHE* 5.9 1.0 - - - -
113C PRO* 3.7 4.7 + - + +
114C VAL* 1.3 72.7 - - - +
116C HIS* 1.3 57.4 + - - +
117C LEU 4.1 0.2 + - - -
202C CU 4.2 6.2 - - - -
16E ARG* 4.9 19.8 - - - +
18E GLN* 6.2 0.2 - - - +
113E PRO* 5.0 13.7 - - - +
114E VAL 4.6 4.9 + - - -
115E ASN* 2.7 63.2 + - - +
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Residues in contact with HIS 116 (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* 3.2 19.9 - - - -
15C HIS* 3.2 30.3 + + + +
35C PHE* 4.7 0.9 - - - -
102C TYR* 3.9 16.6 - + - -
103C ASP 5.5 0.9 - - - -
105C PHE* 4.0 23.3 - + + -
114C VAL* 4.2 5.4 - - + -
115C ASN* 1.3 74.4 - - - +
117C LEU* 1.3 89.3 + - - +
118C ARG* 4.8 1.3 - - + -
202C CU 2.9 24.2 - - - -
37E ARG* 4.1 16.9 + - - -
40E GLU* 3.7 31.3 + - - -
115E ASN* 4.4 0.3 + - - -
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Residues in contact with LEU 117 (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* 3.5 37.9 - - + +
13C LEU 3.5 1.3 - - - -
14C GLY* 4.1 3.6 - - - -
35C PHE* 3.7 27.8 - - + -
37C ARG* 4.0 8.5 - - - +
115C ASN 4.1 0.6 + - - -
116C HIS* 1.3 91.8 + - - +
118C ARG* 1.3 61.1 + - - +
12E GLU* 5.3 0.2 - - - +
37E ARG* 2.9 27.7 + - - +
115E ASN* 3.2 46.0 - - + +
117E LEU* 3.3 24.1 - - + +
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Residues in contact with ARG 118 (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* 3.6 6.8 - - - +
13C LEU* 2.6 47.7 + - + +
100C PHE* 3.7 27.7 - - - +
101C ASP 3.5 25.5 + - - +
102C TYR* 4.1 25.3 - - + +
103C ASP* 4.9 2.2 - - - +
116C HIS* 4.8 1.3 - - - +
117C LEU* 1.3 76.8 - - - +
119C CYS* 1.3 66.9 + - - +
120C GLU* 2.6 39.7 + - + +
12E GLU* 5.1 2.0 - - - +
40E GLU* 3.3 33.3 + - + +
117E LEU* 4.1 1.6 - - - -
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Residues in contact with CYS 119 (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 3.9 4.3 - - - +
12C GLU* 5.2 6.3 - - - +
39C PRO* 6.5 0.7 - - - -
118C ARG* 1.3 75.3 - - - +
120C GLU* 1.3 76.0 + - - +
12E GLU* 4.2 7.5 + - - +
117E LEU* 3.6 25.8 - - - +
119E CYS* 2.0 47.3 - - + -
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Residues in contact with GLU 120 (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 4.2 0.2 - - - +
10C LYS* 3.7 2.7 - - - +
11C LEU* 2.8 44.7 + - + +
13C LEU* 3.9 17.7 - - + -
100C PHE* 3.6 36.7 - - + -
118C ARG* 2.6 44.8 + - + +
119C CYS* 1.3 82.3 - - - +
121C LYS* 1.3 64.7 + - - +
122C LEU* 4.1 1.5 + - - +
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Residues in contact with LYS 121 (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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8C GLN* 3.9 31.6 + - + +
9C VAL 3.8 7.6 - - - +
10C LYS* 4.6 22.4 - - + +
100C PHE* 5.9 0.3 - - - -
120C GLU* 1.3 77.7 + - - +
122C LEU* 1.3 72.2 + - - +
123C THR* 4.2 14.2 + - + +
10E LYS* 5.8 8.2 - - - +
121E LYS* 5.3 18.0 - - - +
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Residues in contact with LEU 122 (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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7C VAL 3.5 1.2 - - - +
8C GLN* 3.2 4.9 - - - +
9C VAL* 2.9 56.0 + - + +
11C LEU* 3.8 32.3 - - + -
47C PHE* 4.8 1.1 - - + -
89C PHE* 3.9 28.0 - - + -
98C VAL* 4.0 28.7 - - + -
100C PHE* 4.0 14.1 - - + -
120C GLU 5.0 1.6 - - - +
121C LYS* 1.3 81.0 - - - +
123C THR* 1.3 62.9 + - - +
124C PHE* 4.1 8.7 - - + -
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Residues in contact with THR 123 (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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6C ALA* 5.7 3.8 - - - -
7C VAL 3.3 5.6 - - - -
8C GLN* 3.9 27.1 - - + +
121C LYS* 4.2 12.3 + - + +
122C LEU* 1.3 77.2 - - - +
124C PHE* 1.3 65.0 + - - +
125C ASN* 3.9 17.7 + - - -
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Residues in contact with PHE 124 (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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5C CYS 3.6 1.2 - - - +
6C ALA* 3.6 2.3 - - - -
7C VAL* 2.7 45.9 + - + +
9C VAL* 4.0 15.3 - - + -
47C PHE* 5.1 0.2 - + - -
89C PHE* 3.7 47.6 - + - -
91C ASN* 4.5 0.9 - - - -
95C PRO* 4.3 24.7 - - + -
122C LEU* 4.1 14.1 - - + -
123C THR* 1.3 75.6 - - - +
125C ASN* 1.3 64.0 + - - +
126C ASN 3.6 0.5 + - - -
127C PRO* 3.7 17.0 - - + +
131C PHE* 3.9 26.7 - + - -
135C LEU* 3.7 26.9 - - + -
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Residues in contact with ASN 125 (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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5C CYS 3.6 3.0 - - - +
6C ALA* 4.0 17.7 - - - +
123C THR* 3.9 15.2 + - - -
124C PHE* 1.3 72.2 - - - +
126C ASN* 1.3 80.9 + - - +
127C PRO* 3.6 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