Contacts of the strand formed by residues 30 - 37 (chain C) in PDB entry 3IKH
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 30 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A GLN* 5.7 3.6 - - - +
108A THR* 4.2 3.8 - - - +
110A ALA* 5.7 7.9 - - + -
15C TRP* 3.5 3.3 - - - -
16C SER* 2.7 45.8 + - - +
28C HIS* 4.0 16.8 - - + +
29C GLY* 1.3 80.2 - - - +
31C LYS* 1.3 73.7 + - - +
32C VAL* 3.3 6.9 + - + +
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Residues in contact with LYS 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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13A GLU* 4.8 1.2 + - - -
63A ASP* 4.5 7.5 + - - +
65A ASN* 3.6 15.6 - - - +
88A GLN* 4.5 29.1 + - - +
89A HIS 4.5 7.0 - - - +
91A ASP* 3.1 24.3 + - - +
108A THR* 4.1 13.5 - - + +
110A ALA* 6.2 1.4 - - - +
13C GLU* 3.4 33.5 + - + +
14C THR 3.6 4.9 - - - +
15C TRP* 3.4 42.2 - - + +
30C VAL* 1.3 78.6 - - - +
32C VAL* 1.3 62.0 + - - +
33C SER 3.7 2.7 - - - +
34C GLN* 4.3 10.3 - - + +
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Residues in contact with VAL 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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88A GLN* 5.8 1.2 + - - -
14C THR* 2.8 25.8 + - + +
16C SER* 3.6 33.0 - - - +
30C VAL* 3.7 8.3 - - + +
31C LYS* 1.3 75.1 - - - +
33C SER* 1.3 68.4 + - - +
97C ASN* 5.9 1.3 - - - +
268C ARG* 5.5 15.0 - - + +
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Residues in contact with SER 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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12C ASP 3.7 0.6 - - - +
13C GLU* 3.3 4.2 - - - +
14C THR* 2.8 43.5 + - - +
31C LYS* 3.7 2.8 - - - +
32C VAL* 1.3 87.1 - - - +
34C GLN* 1.3 70.3 + - - +
35C ASP* 5.6 1.1 - - - +
226C ASP* 5.4 1.2 + - - -
269C GLY* 4.7 16.2 + - - -
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Residues in contact with GLN 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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63A ASP* 4.5 22.9 + - - +
64A SER* 4.8 8.5 + - - -
11C VAL* 4.6 8.6 - - + +
12C ASP 3.0 8.1 - - - +
13C GLU* 2.3 39.4 + - + +
31C LYS* 4.3 13.9 - - + +
33C SER* 1.3 80.8 - - - +
35C ASP* 1.3 66.6 + - - +
65C ASN* 5.7 0.9 - - - +
68C TRP* 4.0 23.2 - - + -
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Residues in contact with ASP 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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11C VAL* 3.3 3.6 - - - -
12C ASP* 2.6 39.2 + - + +
33C SER* 5.6 2.2 - - - +
34C GLN* 1.3 76.5 - - - +
36C ILE* 1.3 78.3 + - - +
68C TRP* 3.9 11.6 - - - -
72C GLN* 5.5 2.1 + - - -
269C GLY* 3.8 4.8 - - - -
270C THR* 2.9 28.7 + - - +
271C LEU* 3.8 7.3 - - - +
272C SER* 2.4 45.6 + - - -
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Residues in contact with ILE 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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9C ILE* 4.5 17.5 - - + -
10C THR 3.6 8.7 - - - +
11C VAL* 4.5 0.4 - - + -
35C ASP* 1.3 80.7 + - - +
37C GLY* 1.3 65.3 + - - +
41C ALA* 5.4 0.4 - - + -
42C ASN* 4.4 0.3 - - - +
45C ILE* 5.2 8.3 - - + -
68C TRP* 3.7 40.2 - - + -
69C ILE* 3.9 26.9 - - + -
72C GLN* 3.6 28.9 - - + +
73C ILE* 5.2 2.0 - - + -
270C THR* 3.2 3.9 - - - -
271C LEU* 3.1 47.7 + - + +
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Residues in contact with GLY 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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9C ILE* 3.5 1.6 - - - +
10C THR* 2.8 34.4 + - - +
12C ASP* 3.8 5.8 - - - -
35C ASP 3.7 1.8 + - - -
36C ILE* 1.3 75.3 - - - +
38C GLY* 1.3 61.6 + - - -
41C ALA* 3.5 16.1 - - - +
42C ASN* 3.3 13.7 - - - -
270C THR* 3.6 9.0 - - - -
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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