Contacts of the helix formed by residues 93 - 101 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84F LEU 6.1 0.2 - - - +
86F GLN 3.6 2.9 - - - +
87F LYS* 3.6 23.1 - - + -
91F GLY 3.6 7.0 - - - +
92F VAL* 1.3 89.8 - - + +
94F PHE* 1.3 67.5 + - - +
95F VAL* 4.2 6.7 - - + +
96F ARG* 2.8 49.5 + - + +
97F THR* 3.1 6.4 + - - -
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Residues in contact with PHE 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57F ARG* 3.4 29.6 - - + -
60F ARG* 4.1 7.9 - - + -
61F GLN* 3.8 23.8 - - + -
64F PHE* 3.3 34.8 - + + -
79F PHE* 3.8 10.3 - - + -
83F THR* 3.9 8.7 - - + +
86F GLN* 3.1 51.0 + - + +
87F LYS 3.8 11.0 - - - -
88F ASP* 3.7 28.3 - - + -
92F VAL 3.2 3.1 + - - -
93F PRO* 1.3 70.7 - - - +
95F VAL* 1.3 61.3 + - - +
97F THR* 3.3 7.7 + - - -
98F ILE* 3.1 29.6 + - - +
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Residues in contact with VAL 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79F PHE* 4.2 12.3 - - + -
84F LEU* 3.2 51.6 - - + +
93F PRO* 3.0 6.3 - - + -
94F PHE* 1.3 78.8 - - - +
96F ARG* 1.3 63.7 + - - +
98F ILE* 3.4 1.6 + - - +
99F GLN* 2.8 50.7 + - + +
105F VAL* 4.0 14.4 - - + -
141F ASP 3.8 20.2 - - - +
142F GLY* 4.6 0.4 - - - -
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Residues in contact with ARG 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92F VAL* 4.1 11.2 - - + +
93F PRO* 2.8 40.9 + - + +
95F VAL* 1.3 79.8 - - - +
97F THR* 1.3 57.0 + - - +
99F GLN* 3.1 16.5 + - - +
100F ASP* 2.8 53.5 + - - +
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Residues in contact with THR 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64F PHE* 3.6 24.9 - - + +
65F SER* 5.6 0.7 - - - -
88F ASP* 4.4 7.8 + - - -
92F VAL* 3.7 15.3 + - - +
93F PRO 3.1 8.4 + - - -
94F PHE* 3.5 12.8 - - - -
96F ARG* 1.3 77.3 - - - +
98F ILE* 1.3 67.1 + - + +
100F ASP* 3.0 19.6 + - - +
101F LYS* 3.2 26.9 + - + +
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Residues in contact with ILE 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64F PHE* 3.5 45.1 - - + +
77F VAL* 3.9 23.3 - - + -
79F PHE* 4.1 12.3 - - + -
94F PHE 3.1 20.6 + - - +
95F VAL 3.9 2.2 - - - +
97F THR* 1.3 81.4 - - + +
99F GLN* 1.3 63.6 + - - +
101F LYS* 3.2 12.5 + - + +
103F ILE* 3.2 55.8 + - + +
104F VAL 4.2 1.3 - - - +
105F VAL* 3.9 14.4 - - + -
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Residues in contact with GLN 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95F VAL* 2.8 37.0 + - - +
96F ARG* 3.3 17.0 - - - +
98F ILE* 1.3 78.1 - - - +
100F ASP* 1.3 61.4 + - - +
102F GLY* 2.8 22.2 + - - -
103F ILE 3.9 7.1 - - - +
105F VAL* 3.7 15.2 - - + +
141F ASP 5.4 0.2 - - - +
142F GLY* 3.7 31.1 + - - -
144F ASP* 5.5 1.0 + - - -
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Residues in contact with ASP 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F LYS* 5.4 1.9 + - - -
96F ARG* 2.8 45.0 + - - +
97F THR* 3.0 9.8 + - - +
99F GLN* 1.3 70.8 - - - +
101F LYS* 1.3 59.3 + - + +
102F GLY* 3.0 9.4 + - - -
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Residues in contact with LYS 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64F PHE 4.4 4.0 - - - -
66F ALA 3.0 29.1 + - - -
67F ASP* 3.5 10.0 - - - +
68F ASP* 3.4 24.7 + - - +
70F VAL* 4.0 21.1 - - + -
71F LYS* 3.3 38.3 - - + +
97F THR* 3.2 28.0 + - + +
98F ILE* 3.7 10.8 - - + +
99F GLN 3.2 1.2 - - - -
100F ASP* 1.3 76.2 - - + +
102F GLY* 1.3 61.3 + - - +
103F ILE* 3.4 12.4 + - + +
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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