Contacts of the strand formed by residues 92 - 99 (chain B) in PDB entry 3FA6
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 LYS 92 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B PHE* 4.3 0.6 - - - -
87B TRP* 3.6 4.3 - - - -
88B GLU* 2.9 60.6 + - + +
89B SER* 3.1 22.5 + - - +
90B GLU 3.5 0.8 + - - -
91B ASN* 1.3 81.6 - - - +
93B MET* 1.3 66.9 + - - +
94B VAL* 4.3 12.1 - - + -
110B THR* 4.5 14.8 - - - -
111B LEU 3.3 11.0 - - - +
112B GLU* 4.0 29.7 + - + +
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Residues in contact with MET 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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3B PHE* 3.7 31.9 - - + -
50B PHE* 3.4 39.3 - - + -
65B PHE* 4.4 8.1 - - - -
67B VAL* 5.0 0.7 - - + -
85B VAL* 3.7 22.7 - - + -
86B LYS 3.3 7.0 - - - +
87B TRP* 3.9 15.1 - - + -
92B LYS* 1.3 73.0 - - - +
94B VAL* 1.3 64.6 + - - +
109B TRP* 3.9 30.5 - - + -
110B THR* 3.3 6.6 - - - -
111B LEU* 2.9 44.4 + - + +
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Residues in contact with VAL 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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84B LEU 3.7 1.7 - - - +
85B VAL* 3.3 3.2 - - - -
86B LYS* 2.9 37.0 + - + +
88B GLU* 3.6 35.4 - - + +
92B LYS* 4.3 7.2 - - - -
93B MET* 1.3 81.7 - - - +
95B CYS* 1.3 67.6 + - - +
96B GLU* 4.1 1.6 + - + +
108B SER* 5.6 4.0 - - - +
109B TRP 3.8 2.7 - - - +
110B THR* 4.0 23.6 - - + -
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Residues in contact with CYS 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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71B PHE* 4.3 0.2 - - - -
73B GLU* 3.8 0.7 - - - -
83B SER* 3.5 32.5 - - - -
84B LEU 3.4 5.2 - - - -
85B VAL* 3.7 15.0 - - + +
94B VAL* 1.3 76.6 - - - +
96B GLU* 1.3 63.6 + - - +
97B GLN* 4.0 3.8 - - - -
108B SER* 3.3 12.5 - - - -
109B TRP* 2.8 74.4 + - + +
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Residues in contact with GLU 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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82B LYS 3.8 0.7 - - - +
83B SER* 3.2 4.5 - - - -
84B LEU* 3.0 62.5 + - + +
86B LYS* 4.9 13.0 + - + +
94B VAL* 4.1 3.1 + - + +
95B CYS* 1.3 73.1 - - - +
97B GLN* 1.3 60.3 + - - +
98B LYS* 4.8 19.1 - - + +
106B LYS* 5.6 7.6 - - - +
107B THR 4.9 0.2 - - - -
108B SER* 4.8 4.7 - - - -
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Residues in contact with GLN 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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73B GLU* 2.9 29.1 + - - -
74B GLN 4.3 6.1 + - - -
75B THR* 4.5 6.3 - - - +
81B CYS* 3.6 21.7 - - + -
82B LYS 3.2 4.0 - - - -
83B SER* 3.5 10.5 - - - +
95B CYS* 4.0 9.4 - - - +
96B GLU* 1.3 78.3 - - - +
98B LYS* 1.3 68.0 + - - +
106B LYS* 5.0 10.0 + - - +
107B THR* 2.7 59.1 + - - +
108B SER* 3.9 4.2 + - - +
109B TRP* 3.5 19.4 - - - -
138B LSR 6.0 0.6 - - - +
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Residues in contact with LYS 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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81B CYS* 3.2 4.4 - - - +
82B LYS* 2.8 49.0 + - + +
96B GLU* 4.8 19.7 - - + +
97B GLN* 1.3 81.4 - - - +
99B LEU* 1.3 67.5 + - - +
100B LEU* 3.4 0.3 + - - +
106B LYS* 6.1 1.4 - - - +
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Residues in contact with LEU 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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75B THR* 4.2 12.3 - - + -
79B ARG* 3.1 49.1 - - + +
80B PRO 3.7 15.0 - - - +
81B CYS* 4.2 1.3 - - + +
97B GLN 4.3 0.4 - - - -
98B LYS* 1.3 76.9 - - - +
100B LEU* 1.3 63.1 + - - +
101B LYS 4.0 15.5 - - - +
102B GLY 3.9 7.8 - - - +
103B GLU* 3.5 34.1 - - - +
104B GLY* 3.5 7.9 - - - +
105B PRO 5.1 4.3 - - - +
107B THR* 6.1 0.4 - - - +
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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