Contacts of the strand formed by residues 59 - 65 (chain B) in PDB entry 6BJV
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 PHE 59 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B GLY* 1.3 73.6 - - - -
60B LYS* 1.3 65.2 + - - +
61B GLU* 3.7 29.4 - - + -
72B ARG 4.0 0.2 - - - +
73B TYR* 3.4 9.0 - - - -
74B LEU* 2.9 55.3 + - + +
76B TYR* 3.9 11.7 - - + -
86B VAL* 3.6 41.7 - - + -
114B ILE* 3.7 21.8 - - + -
115B ARG 3.3 15.7 - - - +
116B PHE* 3.6 17.0 - - + -
141B LYS* 3.9 12.8 - - - -
145B LEU* 3.9 17.3 - - + -
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Residues in contact with LYS 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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18B ARG* 3.8 14.3 - - - +
59B PHE* 1.3 76.6 - - - +
61B GLU* 1.3 65.6 + - - +
62B SER* 6.2 0.7 - - - -
71B LYS* 4.5 24.3 - - - +
72B ARG 3.4 12.6 - - - +
73B TYR* 4.2 11.6 - - + -
113B SER 4.1 0.3 - - - +
114B ILE* 3.2 2.4 - - - +
115B ARG* 2.8 52.0 + - + +
1C U 5.1 4.7 - - + +
2C C 2.7 40.6 + - - +
3C G 4.8 6.1 + - - -
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Residues in contact with GLU 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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30B PHE* 3.3 26.6 - - + -
59B PHE* 3.7 17.0 - - + -
60B LYS* 1.3 77.0 - - - +
62B SER* 1.3 62.4 + - - +
71B LYS* 3.6 2.9 - - - +
72B ARG* 3.0 42.3 + - + +
74B LEU* 3.9 6.2 - - + +
89B SER* 2.7 29.1 + - - -
90B TRP* 3.5 4.2 + - - -
112B TYR* 2.5 37.3 + - + +
113B SER 3.1 7.4 - - - +
114B ILE* 4.3 1.6 - - + -
141B LYS* 3.1 16.2 + - - -
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Residues in contact with SER 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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30B PHE* 4.5 1.6 - - - -
60B LYS* 6.2 0.9 - - - -
61B GLU* 1.3 76.7 - - - +
63B TRP* 1.3 62.5 + - - +
64B GLY 4.6 0.5 + - - -
69B VAL* 3.3 25.8 - - - +
70B PHE 3.3 7.6 - - - -
71B LYS* 4.1 8.3 - - - -
111B THR* 4.5 2.4 + - - -
112B TYR* 3.1 13.6 - - - -
113B SER* 2.7 41.6 + - - -
10D A 4.5 2.6 + - - -
11D A 3.8 20.7 + - - -
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Residues in contact with TRP 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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29B PRO* 4.1 24.9 - - + -
30B PHE* 4.1 23.2 - + + -
62B SER* 1.3 73.4 + - - +
64B GLY* 1.3 58.7 + - - +
65B PHE* 3.8 17.0 - + + -
69B VAL* 3.4 0.9 - - - -
70B PHE* 2.7 42.3 + - - +
90B TRP* 3.5 33.5 - + - -
95B VAL* 3.7 22.9 - - + +
110B CYS* 5.3 0.2 - - + -
111B THR 3.3 28.3 - - - -
112B TYR* 3.3 45.3 - + + -
130B LEU* 4.0 19.7 - - + -
133B LEU* 4.6 7.4 - - + -
134B CYS* 3.9 30.1 - - - -
137B ALA* 4.2 2.7 - - + -
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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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62B SER* 4.6 0.2 + - - -
63B TRP* 1.3 75.3 - - - +
65B PHE* 1.3 66.4 + - - -
66B GLY 3.9 4.5 - - - -
68B VAL 3.3 7.2 - - - -
69B VAL* 4.1 13.2 - - - -
109B GLY 4.7 0.2 - - - -
110B CYS* 3.2 7.8 - - - +
111B THR* 2.7 48.9 + - - +
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Residues in contact with PHE 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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6B GLN* 2.6 26.0 + - - -
29B PRO* 3.6 31.2 - - + -
63B TRP* 3.8 19.1 - + + -
64B GLY* 1.3 74.7 - - - -
66B GLY* 1.3 56.9 + - - +
68B VAL* 2.9 19.8 + - - +
70B PHE* 4.1 14.1 - + - -
95B VAL* 3.7 38.8 - - + -
98B ALA* 4.2 1.3 - - + -
99B ALA* 3.7 25.1 - - + -
102B PHE* 4.1 26.5 - + + -
103B LEU* 4.3 15.0 - - + -
108B VAL* 4.5 1.6 - - - -
110B CYS* 4.1 16.8 - - + -
130B LEU* 4.2 5.6 - - + -
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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