Contacts of the strand formed by residues 30 - 37 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108B THR* 4.0 3.7 - - - +
110B ALA* 5.9 7.0 - - + -
15D TRP* 4.4 2.5 - - - -
16D SER* 2.8 44.6 + - - +
28D HIS* 3.9 14.6 - - + +
29D GLY* 1.3 80.2 - - - +
31D LYS* 1.3 73.8 + - - +
32D VAL* 3.2 12.9 + - + +
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Residues in contact with LYS 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ASP* 4.9 5.6 - - - +
65B ASN* 5.4 2.4 - - - +
88B GLN* 3.4 45.6 + - + +
89B HIS 4.1 10.1 - - - +
91B ASP* 3.9 26.4 - - - +
108B THR* 3.8 20.8 - - + +
110B ALA* 6.3 0.4 - - - +
13D GLU* 3.3 31.6 + - - +
14D THR 3.5 5.8 - - - +
15D TRP* 3.2 32.1 - - + +
30D VAL* 1.3 77.8 - - - +
32D VAL* 1.3 59.3 + - - +
33D SER 3.6 2.2 + - - +
34D GLN* 4.1 19.3 - - - +
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Residues in contact with VAL 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B GLN* 4.6 6.4 + - - -
14D THR* 2.8 47.6 + - + +
16D SER* 3.8 19.3 - - - +
30D VAL* 3.6 21.1 - - + +
31D LYS* 1.3 74.8 - - - +
33D SER* 1.3 68.1 + - - +
97D ASN* 5.6 2.9 - - + +
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Residues in contact with SER 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B GLN* 4.8 7.1 + - - +
12D ASP 4.2 0.4 - - - -
13D GLU* 3.4 4.0 - - - +
14D THR* 2.9 44.0 + - - +
31D LYS* 3.6 3.9 + - - -
32D VAL* 1.3 87.0 - - - +
34D GLN* 1.3 70.5 + - - +
35D ASP* 5.7 1.6 - - - +
226D ASP* 5.3 1.0 + - - -
268D ARG* 6.4 0.9 - - - -
269D GLY* 4.7 16.9 + - - -
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Residues in contact with GLN 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ASP* 3.9 23.5 + - - +
64B SER* 4.6 14.1 + - - -
65B ASN* 5.6 2.6 - - - +
88B GLN* 4.5 11.7 - - - +
11D VAL* 4.6 8.9 - - + +
12D ASP 3.1 9.2 - - - +
13D GLU* 3.0 32.4 + - + +
31D LYS* 4.1 14.6 - - - +
33D SER* 1.3 81.9 - - - +
35D ASP* 1.3 63.2 + - - +
68D TRP* 3.8 25.8 - - + -
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Residues in contact with ASP 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D VAL* 3.3 5.2 - - - +
12D ASP* 2.7 35.6 + - + +
33D SER* 5.7 2.2 - - - +
34D GLN* 1.3 74.2 - - - +
36D ILE* 1.3 82.1 + - - +
68D TRP* 4.1 9.3 - - - -
269D GLY* 3.8 4.9 - - - -
270D THR* 3.0 22.1 + - - +
271D LEU* 3.5 21.6 - - - +
272D SER* 2.8 39.9 + - - -
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Residues in contact with ILE 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D ILE* 4.4 16.2 - - + -
10D THR 3.5 7.9 - - - +
11D VAL* 4.7 0.9 - - + -
35D ASP* 1.3 80.7 + - - +
37D GLY* 1.3 65.2 + - - +
41D ALA* 5.3 0.4 - - + -
42D ASN* 4.4 0.5 - - - +
45D ILE* 5.3 4.9 - - + -
68D TRP* 3.8 36.8 - - + -
69D ILE* 3.9 27.4 - - + -
72D GLN* 3.6 28.3 - - + +
73D ILE* 4.5 9.6 - - + -
270D THR* 3.3 19.5 - - - +
271D LEU* 3.3 31.6 + - + +
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Residues in contact with GLY 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D ILE* 3.6 6.2 - - - +
10D THR* 2.8 31.8 + - - +
12D ASP* 3.4 17.9 - - - -
35D ASP 3.6 1.8 + - - -
36D ILE* 1.3 75.0 - - - +
38D GLY* 1.3 58.9 + - - -
41D ALA* 3.6 9.8 - - - +
42D ASN* 3.4 15.5 - - - -
270D THR* 3.7 0.7 - - - -
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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