Contacts of the strand formed by residues 85 - 94 (chain B) in PDB entry 6P59
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 THR 85 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13B ARG* 3.1 41.4 + - + +
14B VAL 4.7 5.6 - - - +
75B ASN 3.5 7.6 + - - -
76B LEU* 2.8 33.7 + - - +
77B THR 2.8 16.3 + - - -
79B GLU* 3.2 22.3 + - - +
84B GLY* 1.3 73.5 - - - -
86B TYR* 1.3 83.8 + - - +
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Residues in contact with TYR 86 (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 ARG* 3.7 2.3 - - - -
14B VAL* 3.3 24.9 + - - +
16B ARG* 4.0 48.9 + - + -
19B ILE* 3.7 22.7 - - + -
55B HIS* 3.8 19.5 - + - -
73B TYR 3.3 16.6 - - - +
74B TRP* 3.7 30.6 - + + -
75B ASN 5.3 1.1 - - - -
76B LEU* 3.8 5.6 - - - +
83B LEU* 5.7 2.9 - - + -
84B GLY 3.8 14.4 - - - -
85B THR* 1.3 97.6 - - - +
87B GLY* 1.3 59.7 + - - +
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Residues in contact with GLY 87 (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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11B VAL* 4.1 10.5 - - - -
12B TRP 3.0 14.8 - - - -
14B VAL* 4.2 9.1 - - - +
19B ILE* 4.3 2.3 - - - +
72B THR* 3.4 5.0 - - - -
73B TYR* 2.6 41.3 + - - +
76B LEU* 3.9 5.1 - - - +
86B TYR* 1.3 75.5 - - - +
88B ALA* 1.3 57.6 + - - +
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Residues in contact with ALA 88 (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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11B VAL* 3.6 3.5 - - - +
12B TRP* 2.9 35.7 + - - +
14B VAL* 4.6 7.5 - - + +
19B ILE* 5.8 0.2 - - + -
70B VAL* 5.1 1.3 - - + -
71B THR 3.3 9.2 - - - +
72B THR* 4.8 7.0 - - + -
73B TYR* 4.9 1.3 - - - -
87B GLY* 1.3 73.7 - - - +
89B ALA* 1.3 61.9 + - - +
90B LEU* 4.3 11.0 - - + -
215B LEU* 4.0 28.9 - - + -
216B CYS* 4.5 8.3 - - - -
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Residues in contact with ALA 89 (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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9B ARG* 3.6 28.9 + - - +
10B PRO 3.5 21.8 - - - +
11B VAL* 4.1 1.3 - - + -
12B TRP* 4.9 1.8 - - - -
69B LYS 3.7 1.9 - - - +
70B VAL* 3.7 1.4 - - - -
71B THR* 2.8 34.2 + - - +
73B TYR* 3.9 19.7 - - + -
88B ALA* 1.3 74.9 - - - +
90B LEU* 1.3 63.0 + - - +
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Residues in contact with LEU 90 (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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9B ARG* 4.1 0.9 - - - -
10B PRO 5.1 0.6 + - - -
12B TRP* 4.6 6.5 - - + +
68B ILE* 5.5 1.1 - - + -
69B LYS 3.6 4.0 - - - -
70B VAL* 4.3 18.2 - - + +
88B ALA* 4.3 3.1 - - + -
89B ALA* 1.3 87.7 - - - +
91B ALA* 1.3 61.0 + - - +
104B ASP* 3.3 10.1 + - - +
105B ILE* 2.9 44.7 + - + +
107B PRO* 3.6 36.1 - - + -
110B ALA* 3.9 4.0 - - + -
212B LEU* 3.8 33.7 - - + -
216B CYS* 4.1 18.6 - - - -
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Residues in contact with ALA 91 (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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9B ARG* 3.4 9.0 - - - +
68B ILE* 3.2 11.8 - - - +
69B LYS* 2.9 39.8 + - + +
90B LEU* 1.3 75.0 - - - +
92B TYR* 1.3 60.1 + - - +
93B ILE* 4.5 1.8 - - + -
102B PHE* 3.3 39.9 - - + -
103B THR 3.2 8.3 - - - +
105B ILE* 4.0 5.6 - - - -
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Residues in contact with TYR 92 (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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142A ALA* 4.7 4.0 + - - +
143A PHE* 3.6 46.7 + + + -
146A ALA* 5.0 9.2 - - + +
62B LEU* 4.3 19.5 - - + -
66B THR* 3.7 31.3 + - - +
67B LYS 3.7 8.3 - - - -
68B ILE* 4.4 1.6 - - + -
91B ALA* 1.3 74.0 - - - +
93B ILE* 1.3 59.9 + - - +
94B ASP* 3.9 27.8 + - + -
101B TYR* 3.6 10.9 - + - +
102B PHE* 3.5 2.9 - - - -
103B THR* 2.7 35.4 + - - +
105B ILE* 3.9 24.4 - - + +
113B LEU* 4.0 16.8 - - + -
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Residues in contact with ILE 93 (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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77A GLN* 3.8 37.0 - - + +
66B THR* 3.4 6.2 - - - -
67B LYS* 2.9 64.7 + - + +
69B LYS* 4.2 17.7 - - + -
91B ALA* 4.5 4.5 - - + -
92B TYR* 1.3 78.1 - - - +
94B ASP* 1.3 61.9 + - - +
95B GLN* 3.8 24.2 + - + +
100B PRO* 4.6 5.6 - - + -
101B TYR 3.3 6.5 - - - +
102B PHE* 3.7 23.3 - - + -
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Residues in contact with ASP 94 (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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139A ALA* 3.1 29.9 - - + +
142A ALA* 4.2 8.5 - - - +
66B THR* 3.7 14.5 - - - +
92B TYR* 3.9 21.2 + - + -
93B ILE* 1.3 72.6 - - - +
95B GLN* 1.3 62.8 + - - +
96B LYS* 3.2 33.0 + - - +
97B CYS* 3.9 2.6 - - - -
100B PRO* 3.4 3.6 - - - +
101B TYR* 2.7 53.7 + - + +
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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