Contacts of the strand formed by residues 92 - 99 (chain B) in PDB entry 3K8G
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 GLU 92 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B ALA 4.0 0.3 - - - +
86B PHE* 3.2 11.6 - - - -
87B PHE* 2.9 37.3 + - + -
90B SER* 2.6 32.5 + - - +
91B LYS* 1.3 75.8 - - - +
93B PHE* 1.3 59.3 + - - +
94B ARG* 3.0 44.0 + - - +
146B ILE* 3.8 1.6 - - - +
147B PHE 3.3 7.2 - - - +
148B GLY* 4.3 0.2 - - - -
151B LYS 4.2 0.7 - - - +
152B ARG* 3.6 21.1 - - + +
153B GLU* 2.9 29.6 + - - +
281B TYR* 5.0 1.1 - - - -
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Residues in contact with PHE 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B VAL* 6.2 0.7 - - + -
48B LEU* 6.1 6.1 - - + -
84B GLY* 5.8 0.9 - - - -
85B ALA 3.4 9.4 - - - -
86B PHE* 3.7 37.2 - + + -
92B GLU* 1.3 74.3 - - - +
94B ARG* 1.3 62.5 + - - +
95B LEU* 4.3 22.4 - - + +
145B VAL 3.9 0.3 - - - +
146B ILE* 3.4 4.3 - - - +
147B PHE* 2.8 58.4 + + + +
277B ILE* 4.2 15.0 - - + -
278B SER* 5.2 2.9 - - - -
280B LEU* 3.9 23.8 - - + -
281B TYR* 3.8 24.5 - + + -
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Residues in contact with ARG 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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40B VAL* 3.2 27.7 + - + +
41B GLY* 4.3 3.2 - - - -
42B SER 5.1 0.6 + - - -
84B GLY* 3.3 3.6 - - - -
85B ALA 2.9 34.2 + - - +
87B PHE* 3.2 41.5 - - + -
90B SER* 4.7 0.4 + - - -
92B GLU* 3.0 38.9 + - - +
93B PHE* 1.3 77.3 - - - +
95B LEU* 1.3 60.2 + - - +
145B VAL 3.3 5.6 - - - -
146B ILE* 4.4 7.2 - - + -
153B GLU* 3.3 36.1 + - - +
158B MET* 4.2 16.2 - - + -
161B ARG* 3.4 16.3 - - - +
166B ASP* 5.6 0.4 + - - -
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Residues in contact with LEU 95 (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 LEU* 5.5 5.8 - - + -
82B VAL* 4.3 11.2 - - + -
83B TYR 3.2 3.4 - - - +
84B GLY* 3.8 16.6 - - - -
93B PHE* 4.6 22.7 - - + -
94B ARG* 1.3 84.6 - - - +
96B PHE* 1.3 60.5 + - - +
144B CYS* 3.4 4.9 - - - -
145B VAL* 2.7 52.0 + - + +
147B PHE* 6.2 1.8 - - + -
158B MET* 3.4 7.2 - - - +
302B MPD 3.6 39.4 - - + +
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Residues in contact with PHE 96 (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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34B VAL* 3.9 17.5 - - + -
36B PRO* 3.5 34.1 - - + +
39B VAL* 3.7 22.0 - - + -
40B VAL* 3.7 19.0 - - + +
82B VAL* 3.5 1.9 - - - -
83B TYR* 2.8 46.0 + + + +
95B LEU* 1.3 73.9 - - - +
97B GLY* 1.3 73.2 + - - +
98B SER* 4.4 7.0 - - - -
142B PHE* 3.4 39.0 - + + -
143B SER 3.5 2.9 - - - -
144B CYS* 4.1 11.0 - - - -
158B MET* 4.5 1.1 - - + -
162B LEU* 4.0 24.2 - - + -
302B MPD 3.5 2.5 - - - -
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Residues in contact with GLY 97 (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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79B THR* 4.2 1.8 - - - -
81B ALA 3.4 7.4 - - - -
82B VAL* 4.6 0.9 - - - -
96B PHE* 1.3 78.4 - - - +
98B SER* 1.3 61.9 + - - -
101B TYR* 3.7 6.0 + - - -
142B PHE* 3.4 7.1 - - - -
143B SER* 2.9 43.6 + - - +
302B MPD 3.1 14.7 - - - +
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Residues in contact with SER 98 (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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36B PRO* 6.0 0.2 - - - -
79B THR* 3.6 1.9 - - - +
80B THR* 2.8 33.8 + - - -
81B ALA* 2.9 18.6 + - - +
83B TYR* 4.5 15.9 - - - -
96B PHE* 4.2 10.2 + - - -
97B GLY* 1.3 73.0 - - - -
99B GLY* 1.3 59.3 + - - +
101B TYR* 3.8 0.9 - - - -
141B HIS* 3.6 7.5 + - - +
142B PHE* 5.4 3.8 - - - -
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Residues in contact with GLY 99 (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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78B ARG 3.3 13.5 - - - -
80B THR* 4.1 11.2 - - - -
98B SER* 1.3 76.8 + - - +
100B SER* 1.3 66.7 + - - -
101B TYR* 3.7 9.2 - - - -
141B HIS* 2.9 36.0 + - - +
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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