Contacts of the strand formed by residues 70 - 75 (chain B) in PDB entry 3K4H
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 ILE 70 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B THR* 3.4 22.0 - - - +
12B GLY 3.8 5.8 - - - +
47B TYR* 3.8 26.2 - - + -
64B MSE 3.1 59.3 + - + +
68B ARG* 3.5 6.5 - - - +
69B GLN* 1.3 81.1 - - + +
71B GLY* 1.3 63.9 + - - +
72B GLY 3.2 26.0 - - - +
93B PHE* 3.3 20.0 - - + -
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Residues in contact with GLY 71 (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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8B THR* 5.6 0.9 + - - -
9B LYS* 6.4 0.2 - - - -
10B THR 2.8 18.5 + - - +
11B LEU* 5.3 1.3 - - - -
44B TYR* 5.5 2.7 - - - -
69B GLN 3.8 2.6 + - - -
70B ILE* 1.3 72.5 - - - +
72B GLY* 1.3 55.9 + - - +
93B PHE* 3.7 7.4 - - - -
94B PRO* 3.5 12.8 - - - +
262B VAL* 3.4 30.4 - - - +
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Residues in contact with GLY 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B THR 4.1 1.8 + - - -
11B LEU* 3.6 4.5 - - - +
12B GLY 2.8 23.0 + - - -
70B ILE* 3.2 6.5 - - - +
71B GLY* 1.3 76.3 - - - +
73B ILE* 1.3 64.3 + - - -
93B PHE* 3.6 4.5 - - - -
94B PRO 3.3 14.1 - - - -
258B LEU* 3.6 9.6 - - - -
262B VAL* 3.7 13.2 - - - +
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Residues in contact with ILE 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B GLY 3.3 6.1 - - - +
14B VAL* 3.9 15.7 - - + -
61B VAL* 3.9 27.4 - - + -
64B MSE 3.5 36.3 - - + -
65B VAL* 4.5 2.9 - - + -
72B GLY* 1.3 76.3 - - - -
74B ILE* 1.3 74.4 + - - +
75B LEU* 3.9 12.6 - - + -
88B LEU* 4.1 14.8 - - + -
93B PHE* 3.6 20.9 - - + -
94B PRO 3.2 5.7 + - - -
95B PHE* 3.1 11.1 - - + +
96B VAL 3.0 23.4 + - - -
258B LEU* 3.4 8.6 - - - +
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Residues in contact with ILE 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 4.6 5.4 - - + -
12B GLY 2.7 6.3 + - - -
13B LEU* 3.7 25.0 - - + +
14B VAL 3.0 25.3 + - - -
35B ILE* 3.8 26.5 - - + -
73B ILE* 1.3 77.2 - - - +
75B LEU* 1.3 66.5 + - - +
76B LEU* 3.5 27.3 + - + -
96B VAL* 3.5 12.3 - - + +
98B ILE* 4.1 12.1 - - + -
254B ALA* 4.7 4.3 - - + +
255B ALA* 4.3 17.5 - - - +
258B LEU* 3.7 24.7 - - + -
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Residues in contact with LEU 75 (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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14B VAL* 3.7 34.1 - - + -
73B ILE* 3.9 11.2 - - + -
74B ILE* 1.3 73.2 - - - +
76B LEU* 1.3 63.1 + - - +
77B TYR 3.3 7.7 + - - +
82B ASP* 5.2 1.8 - - - +
84B ILE* 3.8 22.4 - - + -
85B ILE* 3.7 30.5 - - + -
88B LEU* 4.2 4.9 - - + -
95B PHE* 3.8 22.4 - - + -
96B VAL 2.9 12.2 + - - +
97B LEU* 3.7 21.4 - - + +
98B ILE* 3.0 26.7 + - - +
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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