Contacts of the strand formed by residues 75 - 82 (chain B) in PDB entry 6IY6
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 GLN 75 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B ALA* 3.7 2.6 - - - +
72B LYS* 3.0 33.5 + - + +
73B GLY 4.1 2.4 - - - +
74B LYS* 1.3 90.2 - - + +
76B CYS* 1.3 59.9 + - - +
77B PHE* 3.7 25.2 - - + -
90B LEU* 4.1 28.4 - - + +
91B VAL 3.9 4.0 - - - -
92B ALA* 4.4 16.2 - - + +
102B VAL* 4.1 3.6 - - - +
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Residues in contact with CYS 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B SER* 4.8 2.5 - - - -
70B ARG 3.8 5.6 - - - -
71B ALA* 3.9 10.1 - - + +
75B GLN* 1.3 73.8 - - - +
77B PHE* 1.3 64.3 + - - +
78B LEU* 3.7 13.9 - - - +
90B LEU* 3.6 4.2 - - - +
91B VAL 2.9 38.6 + - - +
102B VAL* 3.8 20.9 - - + +
105B ALA* 3.9 13.9 - - + -
106B ALA* 3.7 35.2 - - - -
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Residues in contact with PHE 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B THR 4.3 0.2 - - - +
69B SER* 3.4 3.8 - - - -
70B ARG* 2.8 50.8 + - + +
71B ALA* 6.1 0.7 - - - -
72B LYS 6.3 0.4 - - - -
75B GLN* 3.7 27.4 - - + -
76B CYS* 1.3 73.2 - - - +
78B LEU* 1.3 62.1 + - - +
88B GLN* 3.1 39.7 - - + -
89B ALA 3.4 5.4 - - - +
90B LEU* 3.4 39.7 - - + -
136B GLU* 4.1 0.9 - - - -
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Residues in contact with LEU 78 (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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66B VAL* 4.0 26.7 - - + -
68B THR 3.5 8.1 - - - +
69B SER* 4.2 6.5 - - - +
76B CYS* 3.7 13.0 - - - +
77B PHE* 1.3 78.8 - - - +
79B VAL* 1.3 64.3 + - - +
80B LEU* 3.8 10.8 - - + -
88B GLN* 3.6 6.2 - - - +
89B ALA* 2.8 50.6 + - + +
91B VAL* 3.6 30.5 - - + -
105B ALA* 3.9 19.3 - - + +
108B ILE* 4.9 0.2 - - + -
139B VAL* 5.1 0.4 - - + -
142B ILE* 3.9 22.9 - - + -
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Residues in contact with VAL 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B VAL* 3.8 0.8 - - - +
67B HIS* 2.8 52.7 + - + +
68B THR* 2.8 39.4 + - + +
78B LEU* 1.3 73.3 - - - +
80B LEU* 1.3 59.3 + - - +
86B ASN* 3.7 30.3 - - + +
87B VAL 3.5 6.3 - - - +
88B GLN* 5.5 3.6 - - + -
130B CYS* 4.3 13.2 - - - -
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Residues in contact with LEU 80 (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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48B VAL* 4.4 2.9 - - - +
62B VAL* 4.8 8.1 - - + -
64B ALA* 3.8 13.2 - - + -
65B ARG 3.3 8.1 - - - +
66B VAL* 4.6 5.8 - - + -
78B LEU* 3.8 17.9 - - + -
79B VAL* 1.3 68.4 - - - +
81B ARG* 1.3 59.4 + - - +
85B PHE 4.3 0.2 - - - +
86B ASN* 3.2 1.8 - - - -
87B VAL* 2.9 46.9 + - + +
89B ALA* 3.5 28.7 - - + -
114B VAL* 4.0 25.6 - - + -
116B VAL* 3.9 20.4 - - + -
137B LEU* 3.8 21.8 - - + -
142B ILE* 5.6 0.7 - - + -
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Residues in contact with ARG 81 (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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261A ASP* 3.6 16.1 + - - -
64B ALA* 3.3 4.4 - - - +
65B ARG* 2.9 59.5 + - - +
67B HIS* 3.3 43.0 - - + -
79B VAL 3.4 0.4 + - - -
80B LEU* 1.3 72.9 - - - +
82B GLN* 1.3 67.4 + - - +
84B GLN* 4.8 8.3 - - - +
85B PHE 3.3 17.3 - - - +
86B ASN* 4.0 13.2 - - + +
111B GLU* 2.7 32.9 + - - -
188B ARG* 4.1 16.8 + - - +
189B THR* 5.8 0.2 - - - +
190B SER* 6.2 0.7 - - - +
602B PO4 2.7 27.5 + - - -
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Residues in contact with GLN 82 (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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261A ASP* 5.5 1.6 - - - -
263A GLU* 4.7 6.3 + - - -
45B LEU 6.0 0.2 + - - -
46B VAL 4.6 1.5 + - - +
47B ARG* 3.5 23.9 - - - +
48B VAL* 2.7 47.1 + - + +
62B VAL* 5.3 0.5 - - - +
63B ARG 4.2 17.6 + - - +
64B ALA* 4.6 4.5 - - + -
65B ARG* 6.1 1.1 - - - +
81B ARG* 1.3 77.3 - - - +
83B GLN* 1.3 90.8 + - + +
84B GLN 3.5 0.9 - - - -
85B PHE* 2.7 30.1 + - - +
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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