Contacts of the strand formed by residues 65 - 70 (chain B) in PDB entry 1K82
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 GLY 65 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62B LEU* 2.8 33.2 + - - +
63B PRO 3.9 0.2 + - - -
64B GLU* 1.3 79.8 - - - +
66B TRP* 1.3 68.5 + - - -
115B TRP* 3.5 16.9 - - - -
116B THR 3.5 9.4 - - - -
117B LYS 3.5 10.5 - - - -
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Residues in contact with TRP 66 (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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52B GLN* 3.9 20.2 - - - -
59B LEU* 4.0 22.2 - - + -
60B LEU 3.4 8.5 - - - -
61B GLU* 3.4 59.0 - - + -
65B GLY* 1.3 74.3 - - - -
67B ILE* 1.3 67.3 + - - +
68B ILE* 3.9 2.6 + - + -
114B LEU 3.8 0.3 - - - +
115B TRP* 3.4 10.3 - - - -
116B THR* 2.8 46.1 + - + +
117B LYS 3.5 19.8 + - - -
118B GLU* 4.2 5.8 + - - +
119B LEU* 3.6 54.1 - - + +
61D GLU* 4.3 5.2 - - - -
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Residues in contact with ILE 67 (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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22B ILE* 4.1 10.8 - - + -
40B ILE* 3.8 12.6 - - + -
43B LEU* 3.4 30.7 - - + -
58B LEU 3.7 0.5 - - - +
59B LEU* 3.4 5.2 - - - -
60B LEU* 2.9 44.0 + - + +
62B LEU* 3.9 24.9 - - + -
66B TRP* 1.3 74.9 - - - +
68B ILE* 1.3 63.9 + - - +
69B ILE* 3.9 9.1 + - + -
94B LEU* 4.3 10.8 - - + -
113B TRP* 3.7 29.4 - - + -
114B LEU 3.6 3.6 - - - +
115B TRP* 4.0 10.8 - - + -
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Residues in contact with ILE 68 (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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57B TYR* 3.6 30.1 - - + -
58B LEU 3.4 7.0 - - - +
59B LEU* 4.0 16.8 - - + -
66B TRP* 4.7 2.7 - - + +
67B ILE* 1.3 76.4 - - - +
69B ILE* 1.3 64.6 + - - +
70B HIS* 5.7 0.2 - - + -
112B ALA 3.7 1.2 - - - +
113B TRP* 3.4 6.4 - - - -
114B LEU* 2.8 49.2 + - + +
116B THR* 4.1 26.7 - - + -
119B LEU* 5.0 0.4 - - + -
122B HIS* 3.8 34.5 - - + +
124B VAL* 4.2 8.1 - - + -
125B LEU* 4.3 9.6 - - + -
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Residues in contact with ILE 69 (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 ILE* 5.5 0.4 - - + -
56B LYS 4.1 0.7 - - - +
57B TYR* 3.4 5.7 - - - -
58B LEU* 2.7 53.1 + - + +
60B LEU* 4.2 28.9 - - + -
67B ILE* 4.3 8.5 - - + +
68B ILE* 1.3 81.0 - - - +
70B HIS* 1.3 70.0 + - - +
71B LEU* 4.5 6.7 - - + +
77B LEU* 4.3 29.2 - - + -
102B LEU* 4.6 4.9 - - + -
104B TYR* 4.6 1.8 - - + -
112B ALA 3.7 2.5 - - - +
113B TRP* 4.0 48.7 - - + +
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Residues in contact with HIS 70 (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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33B ARG* 5.5 3.4 - - - -
34B TRP* 6.2 1.9 - + + -
56B LYS* 3.6 22.2 - - + +
57B TYR* 3.6 36.3 - + + -
68B ILE* 5.7 0.2 - - + -
69B ILE* 1.3 75.0 - - - +
71B LEU* 1.3 61.5 + - - +
72B GLY* 3.0 36.6 + - - -
104B TYR* 3.6 7.1 + - - -
110B PHE 4.2 8.0 + - - -
111B GLY* 3.2 4.3 - - - -
112B ALA* 3.0 42.5 + - + +
428J G 3.3 17.4 + - - -
429J A 3.1 32.1 + - - -
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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