Contacts of the strand formed by residues 30 - 37 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A TRP* 3.2 6.6 - - - -
16A SER* 2.7 52.8 + - - +
29A GLY* 1.3 79.2 - - - +
31A LYS* 1.3 62.4 + - - +
32A VAL* 3.1 23.2 + - + +
108C THR* 4.9 1.1 - - - -
109C THR* 6.1 1.3 - - - +
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Residues in contact with LYS 31 (chain A).
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* 3.3 19.7 + - - -
14A THR 4.0 5.2 - - - +
15A TRP* 3.8 36.0 - - + +
30A VAL* 1.3 73.6 - - - +
32A VAL* 1.3 62.8 + - - +
33A SER 5.0 6.7 - - - +
34A GLN* 3.0 40.8 - - + +
65A ASN* 5.1 1.0 + - - -
89C HIS* 6.2 3.0 - - + -
92C THR* 4.8 12.3 + - - +
108C THR* 4.1 16.0 - - + +
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Residues in contact with VAL 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A THR* 2.8 36.7 + - + +
16A SER* 4.1 14.8 - - - +
30A VAL* 3.1 19.7 + - + +
31A LYS* 1.3 75.6 - - - +
33A SER* 1.3 67.4 + - - +
96A LEU* 5.7 2.2 - - + -
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Residues in contact with SER 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ASP 4.5 0.2 - - - -
13A GLU* 3.5 3.5 - - - +
14A THR* 2.8 53.0 + - - +
31A LYS* 3.6 4.3 - - - +
32A VAL* 1.3 88.6 - - - +
34A GLN* 1.3 65.4 + - - +
35A ASP* 4.3 11.4 + - - -
118B ASP* 5.6 6.1 - - - -
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Residues in contact with GLN 34 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A VAL* 4.0 13.0 - - + +
12A ASP 3.3 5.4 - - - -
13A GLU* 3.5 21.8 - - + +
31A LYS* 3.0 38.1 - - + +
33A SER* 1.3 79.2 - - - +
35A ASP* 1.3 70.0 + - - +
65A ASN* 3.7 16.0 + - - +
68A TRP* 3.5 42.8 + - + -
118B ASP* 4.7 17.3 + - - +
89C HIS* 6.0 1.6 - - - -
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Residues in contact with ASP 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A VAL* 3.5 2.3 - - - -
12A ASP* 2.7 44.7 + - + +
14A THR* 4.3 11.4 + - - -
33A SER* 4.3 9.1 + - - -
34A GLN* 1.3 90.4 + - - +
36A ILE* 1.3 60.9 + - - +
68A TRP* 3.8 8.7 - - - -
94A ILE* 5.6 1.0 - - - +
269A GLY* 4.5 11.6 - - - -
270A THR* 3.1 35.7 - - + +
271A LEU* 6.2 0.2 - - + -
272A SER* 5.5 2.4 + - - -
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Residues in contact with ILE 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ILE* 4.0 16.2 - - + -
10A THR 3.4 11.0 - - - +
35A ASP* 1.3 71.4 - - - +
37A GLY* 1.3 68.0 + - - +
41A ALA* 4.4 7.4 - - + -
42A ASN* 4.0 1.3 - - - +
45A ILE* 4.5 3.6 - - + -
68A TRP* 3.7 22.6 - - + -
69A ILE* 3.8 16.4 - - + +
72A GLN* 3.4 28.5 - - + -
73A ILE* 3.7 22.7 - - + +
270A THR* 2.8 25.3 + - - -
271A LEU* 3.7 31.4 - - + +
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Residues in contact with GLY 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ILE* 3.9 0.5 - - - +
10A THR* 2.9 37.1 + - - -
12A ASP* 3.5 15.7 - - - -
35A ASP 3.4 2.4 + - - -
36A ILE* 1.3 75.5 - - - +
38A GLY* 1.3 64.5 + - - +
41A ALA* 3.6 13.9 - - - +
42A ASN* 3.9 10.8 - - - -
270A THR* 4.7 0.9 - - - -
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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