Contacts of the strand formed by residues 86 - 93 (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 ARG 86 (chain v).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80v VAL 4.2 3.5 - - - +
82v SER 4.9 5.7 + - - -
84v SER* 3.2 7.8 + - - +
85v GLY* 1.3 76.0 - - - +
87v ILE* 1.3 64.1 + - - +
88v VAL* 3.6 1.8 + - + -
104v GLN* 5.4 7.4 - - + -
105v GLU 3.3 11.4 - - - +
106v THR* 5.4 1.1 - - - -
1156v CYS 3.0 28.1 - - - +
1157v GLY* 3.8 20.9 - - - +
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Residues in contact with ILE 87 (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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80v VAL 3.6 9.0 - - - +
81v GLY* 4.9 5.8 - - - -
85v GLY 4.0 1.6 - - - -
86v ARG* 1.3 72.7 - - - +
88v VAL* 1.3 60.1 + - - +
103v HIS 3.7 1.2 - - - +
104v GLN* 3.5 2.4 - - - -
105v GLU* 2.9 39.9 + - + +
107v PHE* 5.5 6.2 - - + +
132v ILE* 5.7 9.2 - - + -
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Residues in contact with VAL 88 (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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78v ILE 3.6 0.5 - - - +
79v VAL* 3.5 4.5 - - - +
80v VAL* 2.9 40.8 + - + +
86v ARG* 3.6 5.3 + - + +
87v ILE* 1.3 76.2 - - - +
89v ILE* 1.3 62.1 + - - +
90v LEU* 4.3 2.1 + - + +
101v LYS* 6.3 3.1 - - + -
103v HIS 3.3 6.3 - - - +
104v GLN* 4.7 9.4 - - + -
1155v LEU 3.6 24.2 - - - +
1156v CYS* 4.8 5.4 - - - +
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Residues in contact with ILE 89 (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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77v TYR* 5.6 6.5 - - + -
78v ILE 3.1 9.0 - - - +
79v VAL* 4.7 3.4 - - + +
88v VAL* 1.3 74.4 - - - +
90v LEU* 1.3 60.3 + - - +
101v LYS* 3.9 2.6 - - - -
102v ILE* 2.9 33.2 + - + +
103v HIS* 2.9 24.1 + - + +
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Residues in contact with LEU 90 (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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76v ASP 4.9 0.2 - - - +
77v TYR* 3.6 8.4 - - - +
78v ILE* 2.8 46.1 + - + +
80v VAL* 6.5 1.3 - - + -
88v VAL* 5.5 2.2 - - + +
89v ILE* 1.3 75.2 - - - +
91v GLU* 1.3 61.4 + - - +
99v PHE* 4.7 15.9 - - + -
100v GLU 3.5 9.2 - - - +
101v LYS* 5.6 0.9 - - - -
102v ILE* 5.1 1.6 - - - -
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Residues in contact with GLU 91 (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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76v ASP 5.4 4.7 - - - +
77v TYR* 5.7 4.5 - - + -
90v LEU* 1.3 75.8 - - - +
92v TYR* 1.3 63.0 + - - +
99v PHE* 4.6 2.0 - - - -
100v GLU* 2.8 47.1 + - + +
102v ILE* 5.2 7.6 - - + -
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Residues in contact with TYR 92 (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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22v PHE* 3.6 38.7 + - + +
23v SER* 4.8 4.8 - - - +
76v ASP 5.7 1.4 + - - -
91v GLU* 1.3 72.0 - - - +
93v GLN* 1.3 63.1 + - - +
94v PRO 3.7 2.8 - - - -
98v MET 4.1 6.3 - - - +
99v PHE* 4.7 4.5 - - + +
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Residues in contact with GLN 93 (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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91v GLU 3.5 2.8 + - - +
92v TYR* 1.3 71.0 - - - +
94v PRO* 1.3 60.1 - - - +
95v SER* 4.5 5.6 - - - +
96v LYS* 4.7 9.9 - - + +
97v ASN* 3.1 27.6 + - - +
98v MET 3.4 16.1 + - - +
100v GLU* 5.3 7.9 - - + -
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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