Contacts of the strand formed by residues 58 - 67 (chain B) in PDB entry 1I7K
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 ASN 58 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55B GLU* 3.2 30.1 + - - +
56B SER 3.4 0.8 + - - -
57B ASP* 1.3 85.9 - - - +
59B LEU* 1.3 63.3 + - - +
60B PHE* 3.0 38.0 + - - +
61B LYS* 3.2 37.6 + - - +
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Residues in contact with LEU 59 (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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32B GLY* 3.7 37.2 - - - +
35B LEU* 3.4 22.3 - - + +
36B GLN* 4.4 20.9 - - + +
39B LEU* 6.3 0.7 - - + -
54B PRO* 4.0 26.5 - - + -
55B GLU 4.2 0.8 + - - +
58B ASN* 1.3 73.2 - - - +
60B PHE* 1.3 69.2 + - + +
61B LYS 3.3 1.1 - - - -
62B TRP* 2.9 29.3 + - + -
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Residues in contact with PHE 60 (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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31B VAL* 3.7 30.7 - - + -
32B GLY* 4.9 8.5 - - - -
35B LEU* 4.1 16.4 - - + -
58B ASN* 3.0 19.5 - - - +
59B LEU* 1.3 87.4 - - + +
61B LYS* 1.3 58.6 + - - +
84B GLU* 3.5 3.1 - - - +
85B PHE* 2.9 47.2 + - + +
86B PRO 5.5 2.0 - - - -
87B SER* 6.4 2.0 - - - -
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Residues in contact with LYS 61 (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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54B PRO* 3.5 2.1 - - - +
55B GLU* 3.0 54.9 + - + +
58B ASN* 3.2 21.5 + - - +
59B LEU 3.3 0.2 - - - -
60B PHE* 1.3 81.4 - - - +
62B TRP* 1.3 70.2 + - - +
63B VAL* 5.0 8.2 - - + +
82B SER* 4.4 16.5 - - - -
83B LEU 3.4 4.5 - - - +
84B GLU* 2.9 40.4 - - + +
99B LEU* 5.8 3.8 - - - +
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Residues in contact with TRP 62 (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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35B LEU* 3.7 30.5 - - + +
38B GLU* 4.4 2.2 - - + -
39B LEU* 3.7 44.6 - - + -
42B LEU* 4.3 4.9 - - + -
52B ALA* 3.9 25.4 - - + -
53B PHE 3.3 6.1 - - - +
54B PRO* 3.6 23.1 - - + +
55B GLU 4.6 0.4 - - - +
59B LEU* 2.9 28.9 + - + +
61B LYS* 1.3 80.2 - - - +
63B VAL* 1.3 68.5 + - - +
82B SER* 3.4 5.2 - - - -
83B LEU* 2.8 45.9 + - + +
85B PHE* 3.5 22.9 - + - -
128B VAL* 4.1 29.8 - - + -
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Residues in contact with VAL 63 (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 ALA* 3.3 3.1 - - - -
53B PHE* 2.9 30.6 + - - +
54B PRO 5.3 0.2 - - - -
55B GLU* 5.0 14.1 - - + +
61B LYS* 5.0 12.3 - - + +
62B TRP* 1.3 81.5 - - - +
64B GLY* 1.3 67.1 + - - +
65B THR* 5.8 0.2 - - - +
80B LYS* 4.9 20.6 - - + +
81B LEU 3.3 10.8 - - - +
82B SER* 5.0 1.3 - - - -
83B LEU* 4.6 0.2 - - - -
99B LEU* 4.4 20.0 - - + -
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Residues in contact with GLY 64 (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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51B SER 3.1 13.0 - - - -
52B ALA* 3.7 7.9 - - - -
63B VAL* 1.3 75.8 - - - +
65B THR* 1.3 63.2 + - - -
66B ILE* 5.6 0.2 - - - -
80B LYS* 3.3 6.8 - - - +
81B LEU* 2.8 39.4 + - - -
83B LEU* 4.1 7.9 - - - +
132B LEU* 5.3 3.4 - - - -
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Residues in contact with THR 65 (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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49B GLY 3.8 0.6 - - - +
50B ILE* 3.4 4.7 - - - -
51B SER* 2.7 43.6 + - - +
63B VAL* 5.8 0.5 - - - +
64B GLY* 1.3 78.5 + - - -
66B ILE* 1.3 72.3 + - - +
67B HIS* 4.0 23.0 - - + +
78B ARG* 4.3 19.7 + - + +
79B TYR 3.3 10.8 - - - +
80B LYS* 4.0 17.9 - - + +
132B LEU* 5.3 0.5 - - - +
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Residues in contact with ILE 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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49B GLY 3.4 3.6 - - - +
50B ILE* 4.2 7.9 - - + -
65B THR* 1.3 78.3 - - - +
67B HIS* 1.3 75.5 + - - +
78B ARG* 3.2 2.3 - - - +
79B TYR* 2.8 42.0 + - + +
81B LEU* 3.7 25.4 - - + -
98B PHE* 5.7 1.3 - - + -
132B LEU* 3.4 40.2 - - + +
135B ILE* 3.8 23.1 - - + -
136B GLN* 3.7 25.6 - - + +
139B LEU* 4.2 11.4 - - + -
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Residues in contact with HIS 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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49B GLY* 2.9 36.6 + - - +
51B SER* 6.0 1.6 - - - -
65B THR* 4.0 14.8 - - + +
66B ILE* 1.3 84.5 - - - +
68B GLY* 1.3 69.7 + - - +
69B ALA 3.6 0.2 + - - -
76B ASP* 5.9 1.8 - - - -
77B LEU 3.5 6.8 + - - +
78B ARG* 3.6 36.6 + - - +
136B GLN* 3.0 23.6 + - - +
139B LEU* 5.0 0.4 - - - -
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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