Contacts of the strand formed by residues 22 - 32 (chain B) in PDB entry 6FF8
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 ARG 22 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20B GLU* 5.4 2.9 - - + +
21B THR* 1.3 87.7 + - - +
23B GLU* 1.3 60.5 + - - +
24B HIS* 3.9 33.8 + - + -
72B ARG* 2.9 11.4 + - - +
73B THR* 3.4 4.6 - - + +
74B LEU* 2.8 32.9 + - - +
193B LEU* 6.0 1.2 - - - +
196B HIS* 5.8 7.9 - - - +
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Residues in contact with GLU 23 (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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94A VAL* 4.8 4.5 - - - +
21B THR* 5.5 7.7 - - + +
22B ARG* 1.3 76.9 - - - +
24B HIS* 1.3 66.1 + - - +
74B LEU* 3.2 20.2 - - + +
76B ARG* 2.8 39.1 + - - +
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Residues in contact with HIS 24 (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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22B ARG* 3.9 40.4 + - + +
23B GLU* 1.3 76.9 - - - +
25B LEU* 1.3 57.3 - - - +
26B PHE* 3.4 39.5 - + + -
73B THR* 3.7 31.8 - - + +
74B LEU 2.9 10.9 + - - +
75B VAL* 4.3 4.1 - - - +
76B ARG* 2.7 39.0 + - - +
193B LEU* 3.8 14.6 - - + +
196B HIS* 3.8 18.7 - + - +
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Residues in contact with LEU 25 (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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94A VAL* 4.2 22.4 - - + +
97A LYS* 4.2 30.1 - - + -
24B HIS* 1.3 73.1 - - - +
26B PHE* 1.3 68.0 + - - +
27B LYS 4.3 0.3 + - - -
64B LEU* 4.4 2.5 - - + -
76B ARG* 3.2 28.5 - - + +
78B GLN* 3.7 44.0 - - + +
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Residues in contact with PHE 26 (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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24B HIS* 3.4 37.2 - + + -
25B LEU* 1.3 82.0 - - - +
27B LYS* 1.3 57.2 + - - +
28B VAL* 3.6 4.9 + - + -
75B VAL* 3.7 25.1 - - + -
76B ARG 2.8 9.7 + - - -
77B LEU* 3.3 18.4 - - + +
78B GLN* 2.8 34.8 + - - +
100B VAL* 3.7 19.7 - - + -
189B VAL* 4.8 3.6 - - + -
192B ILE* 3.8 33.9 - - + -
193B LEU* 3.9 22.0 - - + -
196B HIS* 3.5 26.9 - + + -
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Residues in contact with LYS 27 (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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25B LEU 4.3 0.6 + - - -
26B PHE* 1.3 70.2 - - - +
28B VAL* 1.3 63.1 + - - +
29B LEU* 4.3 4.9 - - - -
78B GLN* 3.5 16.3 + - + +
80B TRP* 3.5 52.6 - - + +
94B VAL 4.5 1.8 + - - -
95B TYR 2.7 29.2 + - - -
96B TYR 4.3 5.2 - - - -
97B LYS* 2.7 30.2 + - - +
98B GLU* 4.1 11.9 + - + +
99B ALA* 3.4 15.8 - - + +
100B VAL* 3.0 34.0 + - - +
101B GLY 3.6 1.6 + - - -
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Residues in contact with VAL 28 (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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26B PHE 4.1 2.9 - - - +
27B LYS* 1.3 78.1 - - - +
29B LEU* 1.3 75.7 + - - +
77B LEU* 3.9 30.3 - - + -
78B GLN 2.9 9.5 + - - +
79B LEU* 3.5 25.4 - - + +
80B TRP* 2.9 27.5 + - - -
101B GLY 3.5 5.8 - - - +
103B PHE* 4.2 6.3 - - + -
188B LEU* 3.9 24.9 - - + -
192B ILE* 4.0 20.4 - - + -
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Residues in contact with LEU 29 (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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27B LYS* 4.3 5.8 - - - -
28B VAL* 1.3 75.4 - - - +
30B VAL* 1.3 65.3 + - - +
31B ILE* 4.1 9.0 - - + -
80B TRP* 3.6 19.7 - - + -
82B ILE* 4.2 9.2 - - + -
95B TYR 3.9 21.5 - - - +
96B TYR* 3.4 35.2 - - + -
99B ALA* 3.5 26.7 - - + -
101B GLY 3.0 8.4 + - - +
102B ALA* 3.3 6.9 - - + -
103B PHE 2.8 25.7 + - - -
124B LEU* 3.5 21.8 - - + -
128B VAL* 4.9 0.2 - - + -
136B ILE* 4.4 3.1 - - + -
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Residues in contact with VAL 30 (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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28B VAL 4.6 0.4 - - - +
29B LEU* 1.3 77.6 - - - +
31B ILE* 1.3 63.0 + - - +
38B LYS* 3.5 38.1 - - + +
41B ILE* 5.7 4.7 - - + -
42B ILE* 3.7 29.6 - - + -
79B LEU* 4.3 13.2 - - + -
80B TRP 2.9 11.7 + - - +
81B ASP* 4.4 1.1 - - - -
82B ILE 3.2 23.7 + - - -
103B PHE* 3.5 21.5 - - + -
105B VAL* 4.0 16.4 - - + -
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Residues in contact with ILE 31 (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 LEU* 4.2 9.4 - - + -
30B VAL* 1.3 78.5 - - - +
32B GLY* 1.3 60.3 + - - +
38B LYS* 3.5 7.4 - - - -
82B ILE* 3.7 25.6 - - + -
96B TYR* 4.1 15.3 - - + +
102B ALA* 5.2 1.3 - - + -
103B PHE 2.9 16.8 + - - +
104B VAL* 3.4 21.5 - - + -
105B VAL* 3.0 27.9 + - - +
120B TRP* 3.7 46.0 - - + +
124B LEU* 4.1 22.4 - - + -
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Residues in contact with GLY 32 (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 ILE* 1.3 77.6 - - - +
33B GLU* 1.3 67.5 + - - +
36B VAL* 4.2 0.9 - - - -
38B LYS* 3.2 19.1 + - - +
84B GLY* 3.4 2.9 - - - -
104B VAL* 5.2 1.6 - - - -
105B VAL 3.6 14.8 - - - -
120B TRP* 3.3 35.7 - - - -
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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