Contacts of the helix formed by residues 93 - 101 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84G LEU 6.1 0.4 - - - +
85G TYR 6.4 0.2 - - - -
86G GLN 3.6 2.9 - - - +
87G LYS* 3.6 22.8 - - + -
91G GLY 3.6 7.2 - - - +
92G VAL* 1.3 90.3 - - + +
94G PHE* 1.3 67.0 + - - +
95G VAL* 4.2 6.3 - - + +
96G ARG* 2.8 50.0 + - + +
97G THR* 3.1 6.1 + - - -
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Residues in contact with PHE 94 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57G ARG* 3.4 29.6 - - + -
60G ARG* 4.1 7.6 - - + -
61G GLN* 3.8 24.2 - - + -
64G PHE* 3.3 35.0 - + + -
79G PHE* 3.8 10.5 - - + -
83G THR* 3.8 8.1 - - + +
86G GLN* 3.1 50.4 + - + +
87G LYS 3.8 10.8 - - - -
88G ASP* 3.7 27.6 - - + -
92G VAL 3.2 2.5 + - - -
93G PRO* 1.3 70.9 - - - +
95G VAL* 1.3 63.4 + - - +
97G THR* 3.3 7.5 + - - -
98G ILE* 3.1 30.6 + - - +
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Residues in contact with VAL 95 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79G PHE* 4.2 12.1 - - + -
84G LEU* 3.2 51.8 - - + +
86G GLN 5.9 0.2 - - - +
93G PRO* 3.0 6.0 - - + -
94G PHE* 1.3 78.6 - - - +
96G ARG* 1.3 63.2 + - - +
98G ILE* 3.4 1.2 + - - +
99G GLN* 2.8 52.3 + - + +
105G VAL* 4.0 13.9 - - + -
141G ASP 3.8 20.0 - - - +
142G GLY* 4.6 0.4 - - - -
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Residues in contact with ARG 96 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92G VAL* 4.1 11.9 - - + +
93G PRO* 2.8 41.3 + - + +
95G VAL* 1.3 79.0 - - - +
97G THR* 1.3 58.4 + - - +
99G GLN* 3.1 16.9 + - - +
100G ASP* 2.8 53.9 + - - +
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Residues in contact with THR 97 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64G PHE* 3.6 24.9 - - - +
65G SER* 5.6 1.1 - - - -
88G ASP* 4.4 7.8 + - - +
92G VAL* 3.7 15.0 + - - +
93G PRO 3.1 8.8 + - - -
94G PHE* 3.5 13.0 - - - -
96G ARG* 1.3 78.0 - - - +
98G ILE* 1.3 68.7 + - + +
100G ASP* 3.0 19.3 + - - +
101G LYS* 3.2 26.8 + - + +
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Residues in contact with ILE 98 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64G PHE* 3.5 44.6 - - + +
77G VAL* 3.9 23.3 - - + -
79G PHE* 4.1 11.9 - - + -
94G PHE 3.1 20.4 + - - +
95G VAL 3.9 2.5 - - - +
97G THR* 1.3 78.8 - - - +
99G GLN* 1.3 64.1 + - - +
101G LYS* 3.2 13.1 + - + +
103G ILE* 3.2 55.5 + - + +
104G VAL 4.2 1.3 - - - +
105G VAL* 3.9 14.4 - - + -
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Residues in contact with GLN 99 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95G VAL* 2.8 37.4 + - - +
96G ARG* 3.3 17.4 - - - +
98G ILE* 1.3 77.2 - - - +
100G ASP* 1.3 61.0 + - - +
102G GLY* 2.8 22.0 + - - -
103G ILE 3.9 7.9 - - - +
105G VAL* 3.7 15.5 - - + +
142G GLY* 3.7 30.3 + - - -
144G ASP* 5.5 1.2 + - - -
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Residues in contact with ASP 100 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71G LYS* 5.4 2.1 + - - -
96G ARG* 2.8 45.4 + - - +
97G THR* 3.0 10.5 + - - +
99G GLN* 1.3 70.9 - - - +
101G LYS* 1.3 58.4 + - + +
102G GLY* 3.0 9.4 + - - -
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Residues in contact with LYS 101 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64G PHE 4.4 3.8 - - - -
66G ALA* 3.0 28.9 + - - -
67G ASP* 3.5 10.2 - - - +
68G ASP* 3.4 24.7 + - - +
70G VAL* 4.0 21.1 - - + -
71G LYS* 3.3 39.3 - - + +
97G THR* 3.2 27.7 + - - +
98G ILE* 3.7 9.9 - - + +
99G GLN 3.2 0.8 - - - -
100G ASP* 1.3 75.8 - - + +
102G GLY* 1.3 60.8 + - - +
103G ILE* 3.2 13.9 + - + +
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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