Contacts of the strand formed by residues 98 - 106 (chain v) in PDB entry 6FF7
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 MET 98 (chain v).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92v TYR* 4.1 1.7 - - - -
93v GLN* 3.4 25.5 + - - +
96v LYS* 3.5 11.8 - - + +
97v ASN* 1.3 79.5 - - - +
99v PHE* 1.3 66.2 + - - +
100v GLU* 3.3 4.5 + - - +
1184v SER 5.7 5.2 - - - +
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Residues in contact with PHE 99 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90v LEU* 4.7 15.5 - - + -
91v GLU 3.8 7.4 - - - +
92v TYR* 4.7 3.6 - - + +
98v MET* 1.3 72.7 - - - +
100v GLU* 1.3 64.0 + - - +
101v LYS* 3.5 3.6 + - - +
1155v LEU* 6.0 6.9 - - + +
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Residues in contact with GLU 100 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90v LEU* 3.5 4.0 - - - -
91v GLU* 2.8 42.4 + - + +
93v GLN* 5.3 7.4 - - + -
98v MET* 3.3 5.9 + - - +
99v PHE* 1.3 69.2 - - - +
101v LYS* 1.3 62.5 + - - +
102v ILE* 3.1 9.7 + - + +
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Residues in contact with LYS 101 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88v VAL* 6.3 3.1 - - + -
89v ILE 4.1 3.8 - - - -
90v LEU* 5.1 1.6 - - - +
99v PHE 3.5 5.5 + - - +
100v GLU* 1.3 67.6 - - - +
102v ILE* 1.3 65.9 + - - +
103v HIS 3.7 1.8 - - - -
104v GLN* 5.9 7.0 - - + -
1155v LEU* 5.7 8.7 - - - +
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Residues in contact with ILE 102 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89v ILE* 2.9 26.2 + - + +
90v LEU* 4.8 4.5 - - - +
91v GLU* 5.1 6.5 - - + +
100v GLU* 3.1 8.6 + - + +
101v LYS* 1.3 74.5 - - - +
103v HIS* 1.3 60.5 + - + +
152v LEU* 6.1 4.9 - - + -
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Residues in contact with HIS 103 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87v ILE 3.7 1.4 - - - +
88v VAL* 3.3 3.3 - - - -
89v ILE* 2.9 37.0 + - + +
101v LYS* 5.2 2.2 - - - -
102v ILE* 1.3 83.1 - - + +
104v GLN* 1.3 60.6 + - - +
105v GLU* 4.1 3.6 - - + -
154v ILE* 5.6 10.1 - - + -
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Residues in contact with GLN 104 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86v ARG* 5.4 9.4 - - + -
87v ILE 3.5 6.1 - - - +
88v VAL* 4.5 8.7 - - + +
101v LYS* 5.9 6.7 - - + -
103v HIS* 1.3 72.3 - - - +
105v GLU* 1.3 61.1 + - - +
1155v LEU 6.0 1.1 - - - +
1157v GLY* 6.2 2.9 - - - -
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Residues in contact with GLU 105 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85v GLY 3.6 0.2 - - - +
86v ARG* 3.3 6.0 - - - +
87v ILE* 2.9 39.8 + - + +
103v HIS* 4.1 4.0 - - + -
104v GLN* 1.3 76.1 - - - +
106v THR* 1.3 63.3 + - - +
107v PHE* 3.9 1.1 + - - +
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Residues in contact with THR 106 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85v GLY 3.3 8.3 - - - -
86v ARG* 4.7 1.3 - - - +
105v GLU* 1.3 75.1 - - - +
107v PHE* 1.3 62.2 + - - +
108v GLY 5.1 1.8 - - - -
15y ALA* 4.1 19.8 - - - +
16y GLY 5.6 0.5 - - - +
81y ASP 5.8 2.0 - - - -
82y ARG* 5.5 12.1 - - - -
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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