Contacts of the strand formed by residues 66 - 76 (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 66 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61B PRO* 3.7 2.4 - - - +
62B LEU* 2.8 37.2 + - - +
63B GLY 3.0 17.4 + - - +
64B ASN* 3.3 17.0 - - + +
65B ASN* 1.3 79.2 - - - +
67B LYS* 1.3 64.0 + - - +
92B TYR* 3.7 26.2 + - - +
93B ILE 3.4 10.8 - - - -
94B ASP* 3.7 22.7 - - - +
95B GLN* 5.1 1.1 - - - +
96B LYS* 4.2 4.3 - - - +
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Residues in contact with LYS 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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77A GLN* 5.7 3.3 + - - -
59B HIS* 3.1 46.8 + - + +
60B ILE 3.3 15.5 - - - +
61B PRO* 3.9 10.1 - - + -
62B LEU* 4.1 4.9 - - - +
66B THR* 1.3 77.2 - - - +
68B ILE* 1.3 67.3 + - - +
69B LYS* 5.1 2.0 - - - +
92B TYR* 3.7 5.1 - - - -
93B ILE* 2.9 63.1 + - + +
95B GLN* 4.0 28.4 + - - +
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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
----------------------------------------------------------
58B VAL 3.5 1.6 - - - +
59B HIS* 3.5 1.4 - - - -
60B ILE* 2.7 53.5 + - + +
62B LEU* 3.8 22.2 - - + -
67B LYS* 1.3 75.3 - - - +
69B LYS* 1.3 62.3 + - - +
70B VAL* 4.0 21.1 - - + -
90B LEU* 5.5 0.9 - - + -
91B ALA 3.2 15.5 - - - +
92B TYR* 4.4 5.4 - - + -
105B ILE* 3.5 26.5 - - + -
110B ALA* 4.0 24.2 - - + +
113B LEU* 4.2 5.8 - - + -
114B ILE* 4.1 10.5 - - + -
212B LEU* 4.8 6.1 - - + -
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Residues in contact with LYS 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLU* 3.2 32.9 + - - +
77A GLN* 3.6 19.5 - - + +
9B ARG* 4.5 2.9 + - - +
57B GLU* 3.1 25.3 + - + +
58B VAL 3.4 2.2 - - - +
59B HIS* 3.4 39.7 - - + +
67B LYS* 4.2 3.5 + - - -
68B ILE* 1.3 72.7 - - - +
70B VAL* 1.3 62.0 + - - +
71B THR* 3.9 11.9 - - - +
89B ALA 3.7 1.9 - - - +
90B LEU* 3.6 2.3 - - - -
91B ALA* 2.9 37.8 + - + +
93B ILE* 4.2 27.5 - - + +
102B PHE* 4.5 1.3 - - - -
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Residues in contact with VAL 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B TRP* 3.6 36.7 - - + -
56B SER 3.9 0.9 - - - +
57B GLU* 3.3 3.6 - - - -
58B VAL* 2.7 42.2 + - + +
60B ILE* 4.3 9.9 - - + -
68B ILE* 4.0 12.3 - - + -
69B LYS* 1.3 73.9 - - - +
71B THR* 1.3 65.8 + - - +
72B THR* 3.9 3.4 + - + +
88B ALA* 5.1 0.9 - - + -
89B ALA 3.7 2.9 - - - -
90B LEU* 4.3 14.6 - - + +
212B LEU* 4.0 35.2 - - + -
215B LEU* 4.6 6.5 - - + -
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Residues in contact with THR 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLU* 4.6 1.5 + - - +
9B ARG* 3.3 24.1 + - - -
54B SER* 5.4 5.8 - - - -
56B SER 3.6 7.4 - - - +
57B GLU* 3.9 18.7 + - + +
69B LYS* 3.9 13.7 + - - -
70B VAL* 1.3 72.4 - - - +
72B THR* 1.3 71.4 + - - +
73B TYR* 3.5 36.0 + - + +
88B ALA* 3.3 5.2 - - - +
89B ALA 2.8 37.4 + - - -
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Residues in contact with THR 72 (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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19B ILE* 4.3 19.7 - - + -
22B TRP* 4.7 13.5 - - + -
23B HIS* 3.7 22.7 - - + +
54B SER* 3.7 1.0 - - - -
55B HIS* 2.7 39.4 + - - +
56B SER* 2.6 49.5 + - - +
70B VAL* 5.0 4.3 - - + +
71B THR* 1.3 82.4 - - - +
73B TYR* 1.3 56.1 + - - +
87B GLY 3.4 6.5 - - - +
88B ALA* 4.8 7.2 - - + -
215B LEU* 5.3 2.0 - - + -
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Residues in contact with TYR 73 (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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69A PHE* 3.8 24.8 - + - -
74A GLN* 4.0 21.6 + - - +
75A GLY 4.8 1.6 + - - -
76A GLU* 4.1 6.2 + - - +
9B ARG* 3.4 25.0 + - - +
11B VAL* 3.8 33.2 - - + -
19B ILE* 4.6 1.2 - - - +
53B TRP* 3.1 30.5 - - + +
54B SER* 4.2 2.0 - - - -
55B HIS* 3.9 2.7 - - - +
71B THR* 3.5 25.7 - - + +
72B THR* 1.3 76.1 - - - +
74B TRP* 1.3 60.7 + - - +
76B LEU* 4.2 19.7 - - + -
86B TYR* 3.3 10.7 - - - +
87B GLY 2.6 37.7 + - - +
89B ALA* 3.9 12.3 - - + -
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Residues in contact with TRP 74 (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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201A MES 5.4 8.1 - - - -
45B HIS* 6.3 0.4 - - - +
52B TRP* 3.2 47.2 + + - -
53B TRP* 2.9 38.7 + - - +
54B SER 3.9 14.6 + - - -
55B HIS* 3.7 16.2 - + + -
73B TYR* 1.3 74.3 - - - +
75B ASN* 1.3 97.6 + - + +
76B LEU* 3.3 4.1 - - - +
83B LEU 6.0 1.8 - - - -
85B THR 4.0 5.4 - - - -
86B TYR* 3.7 32.1 - + + -
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Residues in contact with ASN 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ARG* 5.6 0.6 - - - +
54A GLU* 3.7 2.9 - - - +
201A MES 3.7 32.4 + - - +
52B TRP* 3.7 35.2 - - + -
53B TRP* 3.0 21.3 + - + +
74B TRP* 1.3 109.3 - - + +
76B LEU* 1.3 66.2 + - - +
83B LEU 4.5 6.8 - - - +
84B GLY* 5.0 6.9 - - - -
85B THR 3.5 3.8 + - - -
86B TYR* 5.3 2.4 - - - -
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Residues in contact with LEU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A GLU* 3.5 5.4 - - + -
67A GLN* 3.2 27.6 - - - +
69A PHE* 3.9 16.6 - - + -
11B VAL* 4.6 7.0 - - + -
13B ARG* 4.1 14.1 - - + +
53B TRP* 3.8 20.2 - - + +
73B TYR* 4.2 10.8 - - + -
74B TRP 4.3 4.9 - - - +
75B ASN* 1.3 83.1 - - - +
77B THR* 1.3 70.2 + - - +
78B THR* 3.1 3.5 + - - -
84B GLY* 3.3 5.4 - - - -
85B THR* 2.8 29.9 + - - +
86B TYR 3.8 29.2 - - - +
87B GLY* 3.9 8.3 - - - +
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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