Contacts of the strand formed by residues 10 - 16 (chain B) 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 THR 10 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8B ASN* 4.2 12.3 - - - +
9B ILE* 1.3 81.0 - - - +
11B VAL* 1.3 57.9 + - - +
12B ASP* 2.8 24.5 + - - -
36B ILE* 3.4 8.1 - - - +
37B GLY 2.8 33.5 + - - -
38B GLY* 3.4 14.9 + - - -
69B ILE* 3.7 15.0 - - - +
90B SER* 3.1 27.1 - - - +
91B ASP* 3.7 10.1 - - - +
92B THR* 6.2 0.4 - - + -
107B THR* 5.8 4.7 - - + -
108B THR 5.4 1.6 - - - +
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Residues in contact with VAL 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B THR* 1.3 73.4 - - - +
12B ASP* 1.3 61.0 + - - +
13B GLU* 3.6 12.7 + - + +
34B GLN* 3.3 38.6 - - + -
35B ASP 3.3 5.4 - - - +
65B ASN* 3.5 27.6 - - + +
68B TRP* 3.7 15.7 - - + -
69B ILE* 3.5 28.0 - - + -
90B SER 3.4 4.4 + - - -
91B ASP* 2.8 31.0 - - + +
92B THR 3.0 8.0 + - - +
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Residues in contact with ASP 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B THR* 2.8 22.7 + - - -
11B VAL* 1.3 71.2 - - - +
13B GLU* 1.3 61.3 + - - +
14B THR* 3.9 2.3 + - - -
33B SER 4.0 0.3 - - - +
34B GLN* 3.6 2.9 - - - -
35B ASP* 2.7 35.8 + - + +
37B GLY* 3.6 7.4 - - - -
38B GLY 4.5 2.3 + - - -
92B THR* 2.6 32.8 - - + +
94B ILE* 4.2 10.4 - - + +
228B THR* 4.7 4.7 - - - +
270B THR* 2.8 38.4 + - - +
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Residues in contact with GLU 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B VAL* 3.7 18.6 - - + +
12B ASP* 1.3 69.8 - - - +
14B THR* 1.3 58.2 + - - +
15B TRP* 3.2 26.1 + - + +
31B LYS* 3.0 31.2 + - - -
33B SER 3.7 4.7 - - - +
34B GLN* 3.7 11.7 - - + +
65B ASN* 3.6 24.9 + - - +
91B ASP* 4.7 6.3 - - + +
92B THR* 2.7 16.2 + - - +
93B SER* 3.5 3.7 - - - -
94B ILE* 2.6 35.5 + - - +
13D GLU* 4.7 13.9 - - - +
15D TRP* 5.5 4.3 - - - -
94D ILE* 5.5 0.7 - - - +
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Residues in contact with THR 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ASP 3.9 2.0 + - - -
13B GLU* 1.3 69.7 - - - +
15B TRP* 1.3 61.5 + - - +
31B LYS* 3.5 2.1 - - - +
32B VAL* 2.7 52.6 + - + +
33B SER* 3.0 30.1 + - - +
94B ILE* 3.7 28.7 - - + +
96B LEU* 5.2 10.8 - - + -
269B GLY* 5.8 3.8 - - - -
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Residues in contact with TRP 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B GLU* 3.2 42.2 + - + +
14B THR* 1.3 82.1 - - - +
16B SER* 1.3 61.1 + - - +
17B ILE* 4.8 6.5 - - + -
29B GLY* 4.9 0.7 - - - -
30B VAL 3.2 9.4 - - - -
31B LYS* 4.1 29.1 - - + +
32B VAL* 4.0 2.5 - - - -
93B SER* 4.1 10.0 + - - -
94B ILE 2.8 13.5 + - - +
95B ILE* 4.7 8.1 - - + -
96B LEU* 2.9 30.6 + - - +
13D GLU* 5.4 2.2 - - - -
92D THR* 3.6 32.3 - - - -
94D ILE* 3.4 41.3 - - + +
106D ILE* 4.1 32.5 - - + -
107D THR 4.9 0.2 - - - -
108D THR* 4.6 14.1 - - - -
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Residues in contact with SER 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B TRP* 1.3 73.4 - - - +
17B ILE* 1.3 67.1 + - - +
29B GLY* 3.5 1.7 - - - -
30B VAL* 2.7 45.9 + - - +
32B VAL* 3.6 18.6 - - - -
96B LEU* 3.6 16.6 + - - +
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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