Contacts of the helix formed by residues 92 - 102 (chain A) in PDB entry 2FRV
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 MET 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A HIS 4.7 0.4 - - - +
14A ASN* 2.9 57.2 - - - +
15A ALA 3.8 3.1 - - - -
76A ILE* 4.3 1.8 - - + -
77A PRO* 4.1 17.5 - - + -
82A GLY 4.6 0.6 + - - -
85A GLY* 3.0 43.3 + - - +
86A LYS* 3.7 6.7 - - - +
87A VAL* 4.6 10.8 - - + -
90A ARG 3.4 0.4 + - - -
91A ASN* 1.3 68.1 - - - +
93A TYR* 1.3 64.6 + - - +
95A ILE* 3.3 9.2 + - + +
96A CYS* 3.1 27.4 + - - -
20B HIS* 3.6 32.1 - - + +
41B LEU* 4.0 7.4 - - + -
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Residues in contact with TYR 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A ILE* 3.5 24.2 - - + +
77A PRO 4.2 12.3 + - - +
78A MET* 3.7 26.2 - - + -
81A GLY 5.8 1.6 - - - +
82A GLY* 5.7 2.0 - - - -
91A ASN* 3.2 6.9 - - + +
92A MET* 1.3 79.5 - - - +
94A ASP* 1.3 73.2 + - - +
96A CYS* 3.5 1.6 + - - +
97A ALA* 2.9 38.5 + - + +
134A ALA* 3.7 10.1 - - + -
135A LEU* 3.3 26.0 - - + -
137A LYS* 2.8 33.2 + - - -
138A LEU* 3.9 10.0 - - - +
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Residues in contact with ASP 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ARG* 3.8 18.7 + - + +
91A ASN* 2.8 36.2 + - - +
93A TYR* 1.3 88.5 - - - +
95A ILE* 1.3 64.5 + - - +
97A ALA* 3.3 5.5 + - - +
98A GLU* 3.1 22.9 + - - +
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Residues in contact with ILE 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LEU* 4.3 18.6 - - + -
57A GLU* 5.7 4.5 - - - +
60A LEU* 4.3 11.4 - - + -
87A VAL* 3.6 38.1 - - + +
90A ARG* 3.4 54.5 - - + +
91A ASN 3.1 10.3 + - - +
92A MET* 3.3 7.8 + - + +
94A ASP* 1.3 76.4 - - - +
96A CYS* 1.3 57.0 + - - +
98A GLU* 3.2 2.1 + - - +
99A VAL* 2.9 40.8 + - + +
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Residues in contact with CYS 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LEU* 4.0 20.2 - - - -
14A ASN* 3.4 32.1 - - - -
72A ILE* 4.4 6.3 - - + -
76A ILE* 3.9 16.8 - - + -
92A MET 3.1 19.9 + - - +
93A TYR 3.8 2.9 - - - +
95A ILE* 1.3 73.5 - - - +
97A ALA* 1.3 63.8 + - - +
99A VAL 4.4 0.4 - - - +
100A ALA* 2.9 36.2 + - - +
135A LEU* 3.7 20.3 - - + +
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Residues in contact with ALA 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A TYR* 2.9 36.4 + - + +
94A ASP* 3.3 6.0 + - - +
96A CYS* 1.3 77.7 - - - +
98A GLU* 1.3 56.6 + - - +
101A PRO* 2.9 25.3 - - - +
135A LEU* 4.4 2.2 - - - +
138A LEU* 3.4 29.0 - - + +
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Residues in contact with GLU 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A LEU* 6.5 0.2 - - - -
61A HIS* 4.8 10.4 + - - -
64A ILE* 3.7 25.7 - - + +
90A ARG* 2.7 39.4 + - - +
94A ASP 3.1 10.1 + - - +
95A ILE* 3.5 7.9 - - - +
97A ALA* 1.3 80.1 - - - +
99A VAL* 1.3 66.3 + - + +
101A PRO* 3.8 2.3 - - - +
102A LYS* 3.1 37.4 + - - +
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Residues in contact with VAL 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A VAL* 4.2 7.0 - - + -
12A LEU* 4.1 12.8 - - + -
60A LEU* 4.4 10.5 - - + -
64A ILE* 3.9 29.2 - - + -
68A PHE* 3.7 17.2 - - + -
70A CYS* 4.0 20.2 - - - -
95A ILE* 2.9 36.6 + - + +
98A GLU* 1.3 78.0 - - + +
100A ALA* 1.3 68.1 + - - +
102A LYS* 3.0 22.5 + - - +
103A ALA 3.6 4.2 + - - -
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Residues in contact with ALA 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A CYS* 4.3 8.5 - - - -
72A ILE* 4.1 17.5 - - + -
96A CYS* 2.9 20.8 + - - +
99A VAL* 1.3 76.7 - - - +
101A PRO* 1.3 67.0 - - + +
103A ALA* 3.2 21.1 + - - +
106A VAL* 3.6 14.0 - - + +
135A LEU* 4.0 12.8 - - + -
140A VAL* 3.9 18.6 - - + +
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Residues in contact with PRO 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A CYS 3.4 0.7 - - - +
97A ALA 2.9 29.4 - - - +
98A GLU 3.8 2.5 - - - +
99A VAL 3.4 3.6 - - - -
100A ALA* 1.3 95.8 - - + +
102A LYS* 1.3 60.2 + - + +
103A ALA 3.5 4.5 + - - +
138A LEU* 4.0 37.0 - - + +
140A VAL* 4.2 9.2 - - + -
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Residues in contact with LYS 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ILE* 3.9 42.6 - - + +
66A GLY 4.4 5.4 - - - +
68A PHE* 3.6 17.2 - - + -
98A GLU* 3.1 33.0 + - - +
99A VAL 3.0 7.1 + - - +
101A PRO* 1.3 77.6 - - + +
103A ALA* 1.3 60.8 + - - +
104A LYS* 4.5 7.8 - - - -
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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