Contacts of the helix formed by residues 93 - 101 (chain J) in PDB entry 1XFB
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 PRO 93 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84J LEU 6.1 0.2 - - - +
85J TYR 6.4 0.4 - - - -
86J GLN 3.6 2.5 - - - +
87J LYS* 3.6 23.3 - - + -
91J GLY 3.6 7.2 - - - +
92J VAL* 1.3 90.1 - - + +
94J PHE* 1.3 67.2 + - - +
95J VAL* 4.2 6.7 - - + +
96J ARG* 2.8 50.7 + - + +
97J THR* 3.1 5.9 + - - -
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Residues in contact with PHE 94 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57J ARG* 3.4 28.9 - - + -
60J ARG* 4.1 6.5 - - + -
61J GLN* 3.8 24.0 - - + -
64J PHE* 3.3 35.2 - + + -
79J PHE* 3.8 10.1 - - + -
83J THR* 3.9 8.7 - - + +
86J GLN* 3.1 50.0 + - + +
87J LYS 3.8 10.8 - - - -
88J ASP* 3.7 29.4 - - + -
92J VAL 3.2 2.2 + - - -
93J PRO* 1.3 71.6 - - - +
95J VAL* 1.3 62.8 + - - +
97J THR* 3.3 7.3 + - - -
98J ILE* 3.1 29.5 + - - +
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Residues in contact with VAL 95 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79J PHE* 4.2 12.3 - - + -
84J LEU* 3.2 52.0 - - + +
86J GLN 5.9 0.2 - - - +
93J PRO* 3.0 6.4 - - + -
94J PHE* 1.3 79.5 - - - +
96J ARG* 1.3 63.2 + - - +
98J ILE* 3.4 1.7 + - - +
99J GLN* 2.8 51.4 + - + +
105J VAL* 4.0 13.7 - - + -
141J ASP 3.8 19.1 - - - +
142J GLY* 4.6 0.7 - - - -
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Residues in contact with ARG 96 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92J VAL* 4.1 11.4 - - + +
93J PRO* 2.8 40.8 + - + +
95J VAL* 1.3 79.6 - - - +
97J THR* 1.3 58.4 + - - +
99J GLN* 3.1 16.9 + - - +
100J ASP* 2.8 53.2 + - - +
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Residues in contact with THR 97 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64J PHE* 3.6 25.6 - - - +
65J SER* 5.6 1.1 - - - -
88J ASP* 4.4 7.6 + - - +
92J VAL* 3.7 15.4 + - - +
93J PRO 3.1 8.6 + - - -
94J PHE* 3.5 13.6 - - - -
96J ARG* 1.3 77.3 - - - +
98J ILE* 1.3 67.9 + - + +
100J ASP* 3.0 18.8 + - - +
101J LYS* 3.2 26.7 + - + +
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Residues in contact with ILE 98 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64J PHE* 3.5 44.9 - - + +
77J VAL* 3.9 22.9 - - + -
79J PHE* 4.1 11.9 - - + -
94J PHE 3.1 20.6 + - - +
95J VAL 3.9 2.5 - - - +
97J THR* 1.3 80.4 - - + +
99J GLN* 1.3 62.7 + - - +
101J LYS* 3.2 13.2 + - + +
103J ILE* 3.2 55.2 + - + +
104J VAL 4.2 1.1 - - - +
105J VAL* 3.9 15.0 - - + -
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Residues in contact with GLN 99 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95J VAL* 2.8 36.9 + - - +
96J ARG* 3.3 16.5 - - - +
98J ILE* 1.3 78.1 - - - +
100J ASP* 1.3 60.7 + - - +
102J GLY* 2.8 22.2 + - - -
103J ILE 3.9 7.4 - - - +
105J VAL* 3.7 15.0 - - + -
141J ASP 5.4 0.2 - - - +
142J GLY* 3.7 30.9 + - - -
144J ASP* 5.5 1.2 + - - -
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Residues in contact with ASP 100 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71J LYS* 5.4 1.9 + - - -
96J ARG* 2.8 45.7 + - - +
97J THR* 3.0 9.8 + - - +
99J GLN* 1.3 70.1 - - - +
101J LYS* 1.3 59.7 + - + +
102J GLY* 3.0 9.2 + - - -
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Residues in contact with LYS 101 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64J PHE 4.4 3.6 - - - -
65J SER 5.4 0.2 - - - -
66J ALA* 3.0 29.3 + - - -
67J ASP* 3.5 10.0 - - - +
68J ASP* 3.4 24.6 + - - +
70J VAL* 4.0 20.9 - - + -
71J LYS* 3.3 39.7 - - + +
97J THR* 3.2 28.4 + - - +
98J ILE* 3.7 10.1 - - - +
99J GLN 3.2 1.0 - - - -
100J ASP* 1.3 75.0 - - + +
102J GLY* 1.3 61.7 + - - +
103J ILE* 3.2 12.7 + - + +
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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