Contacts of the helix formed by residues 93 - 101 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85B TYR 6.4 0.4 - - - -
86B GLN 3.6 2.7 - - - +
87B LYS* 3.6 23.0 - - + -
91B GLY 3.6 7.4 - - - +
92B VAL* 1.3 89.5 - - + +
94B PHE* 1.3 67.0 + - - +
95B VAL* 3.0 6.5 - - + +
96B ARG* 2.8 49.5 + - + +
97B THR* 3.1 6.2 + - - -
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Residues in contact with PHE 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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57B ARG* 3.4 30.1 - - + -
60B ARG* 4.1 7.4 - - + -
61B GLN* 3.8 24.5 - - + -
64B PHE* 3.3 33.0 - + + -
79B PHE* 3.8 9.9 - - + -
83B THR* 3.9 8.5 - - + +
86B GLN* 3.1 49.6 + - + +
87B LYS 3.8 10.1 - - - -
88B ASP* 3.7 29.4 - - + -
92B VAL 3.2 2.4 + - - -
93B PRO* 1.3 71.3 - - - +
95B VAL* 1.3 62.9 + - - +
97B THR* 3.3 7.5 + - - -
98B ILE* 3.1 30.0 + - - +
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Residues in contact with VAL 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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79B PHE* 4.2 12.6 - - + -
84B LEU* 3.2 52.3 - - + +
93B PRO* 3.0 6.6 - - + -
94B PHE* 1.3 78.8 - - - +
96B ARG* 1.3 63.1 + - - +
98B ILE* 3.4 1.4 + - - +
99B GLN* 2.8 51.2 + - + +
105B VAL* 4.0 14.4 - - + -
141B ASP 3.8 19.1 - - - +
142B GLY* 4.6 0.4 - - - -
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Residues in contact with ARG 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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92B VAL* 4.1 11.9 - - + +
93B PRO* 2.8 40.3 + - + +
95B VAL* 1.3 79.0 - - - +
97B THR* 1.3 57.5 + - - +
99B GLN* 3.1 16.7 + - - +
100B ASP* 2.8 53.8 + - - +
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Residues in contact with THR 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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64B PHE* 3.6 25.1 - - + +
65B SER* 5.6 1.1 - - - -
88B ASP* 4.4 7.6 + - - +
92B VAL* 3.7 15.0 + - - +
93B PRO 3.1 9.1 + - - -
94B PHE* 3.5 13.4 - - - -
96B ARG* 1.3 78.4 - - - +
98B ILE* 1.3 68.9 + - + +
100B ASP* 3.0 20.2 + - - +
101B LYS* 3.2 25.9 + - + +
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Residues in contact with ILE 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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64B PHE* 3.5 44.0 - - + +
77B VAL* 3.9 22.9 - - + -
79B PHE* 4.1 12.3 - - + -
94B PHE 3.1 20.2 + - - +
95B VAL 3.9 2.7 - - - +
97B THR* 1.3 81.4 - - - +
99B GLN* 1.3 62.2 + - - +
101B LYS* 3.2 12.5 + - + +
103B ILE* 3.2 55.1 + - + +
104B VAL 4.2 1.6 - - - +
105B VAL* 3.9 14.6 - - + -
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Residues in contact with GLN 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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95B VAL* 2.8 37.7 + - - +
96B ARG* 3.3 16.8 - - - +
98B ILE* 1.3 75.9 - - - +
100B ASP* 1.3 62.1 + - - +
102B GLY* 2.8 21.7 + - - -
103B ILE 3.9 7.8 - - - +
105B VAL* 3.7 15.5 - - + -
142B GLY* 3.7 31.1 + - - -
144B ASP* 5.5 1.2 + - - -
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Residues in contact with ASP 100 (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 LYS* 5.4 2.1 + - - -
96B ARG* 2.8 44.5 + - - +
97B THR* 3.0 10.1 + - - +
99B GLN* 1.3 69.5 - - - +
101B LYS* 1.3 59.3 + - + +
102B GLY* 3.0 9.3 + - - -
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Residues in contact with LYS 101 (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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64B PHE 4.4 4.0 - - - -
66B ALA 3.0 29.1 + - - -
67B ASP* 3.5 10.4 - - - +
68B ASP* 3.4 25.1 + - - +
70B VAL* 4.0 21.5 - - + -
71B LYS* 3.3 38.7 - - + +
97B THR* 3.2 28.5 + - + +
98B ILE* 3.7 10.3 - - + +
99B GLN 3.2 1.0 - - - -
100B ASP* 1.3 76.9 - - + +
102B GLY* 1.3 61.0 + - - +
103B ILE* 3.2 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