Contacts of the helix formed by residues 96 - 109 (chain A) in PDB entry 5V35
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 VAL 96 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A TRP* 6.0 5.2 - - + -
93A HIS 4.5 12.8 - - - +
95A GLY* 1.3 73.4 - - - +
97A TYR* 1.3 70.2 + - - +
98A PRO* 3.2 2.0 - - - -
99A ILE* 3.0 31.1 + - + +
100A LEU* 3.1 19.3 + - + +
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Residues in contact with TYR 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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37A PHE* 3.6 6.6 - + - -
39A THR* 2.9 31.7 + - + -
49A ILE* 4.1 7.6 - - + -
50A ASP* 2.6 36.7 + - - +
93A HIS 5.6 0.4 - - - +
94A THR* 3.1 18.3 + - - +
96A VAL* 1.3 80.0 - - - +
98A PRO* 1.3 65.1 - - + +
100A LEU* 2.9 20.7 + - + +
101A SER* 2.7 42.8 + - - -
104A LEU* 5.0 2.7 - - + +
140A LEU* 4.1 11.7 - - + -
147A LEU* 3.9 22.4 - - + -
149A PHE* 3.7 24.5 - + + -
201A FAR 4.2 13.2 - - + -
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Residues in contact with PRO 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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94A THR 3.8 4.7 - - - +
95A GLY* 3.6 12.1 - - - +
96A VAL 3.5 3.1 - - - -
97A TYR* 1.3 94.1 - - + +
99A ILE* 1.3 58.3 + - - +
101A SER* 3.7 6.1 - - - -
102A ARG* 2.9 28.6 + - - +
132A LEU* 3.7 26.9 - - + +
137A LEU* 3.8 24.1 - - + +
140A LEU* 3.8 27.1 - - + +
141A GLN* 3.6 16.6 - - - +
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Residues in contact with ILE 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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95A GLY 5.3 0.9 - - - +
96A VAL* 3.0 23.7 + - + +
98A PRO* 1.3 74.9 - - - +
100A LEU* 1.3 68.6 + - - +
102A ARG* 3.5 9.2 + - + +
103A SER* 3.2 24.5 + - - +
126A MET* 5.0 7.2 - - + -
132A LEU* 3.6 24.7 - - + -
141A GLN* 4.1 17.7 - - - +
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Residues in contact with LEU 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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72A TRP* 4.2 23.8 - - + -
96A VAL* 3.1 21.6 + - + +
97A TYR* 2.9 24.0 + - + +
99A ILE* 1.3 77.0 - - - +
101A SER* 1.3 59.5 + - - +
103A SER* 2.8 28.0 + - - -
104A LEU* 3.0 22.2 + - + +
201A FAR 3.4 55.2 - - + -
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Residues in contact with SER 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ASP* 2.8 28.4 + - - -
97A TYR* 2.7 26.1 + - - -
98A PRO 3.7 0.2 - - - -
100A LEU* 1.3 73.2 - - - +
102A ARG* 1.3 63.6 + - - +
104A LEU* 3.0 13.6 + - - +
105A ARG* 2.9 42.1 + - - +
137A LEU* 3.3 20.1 - - - +
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Residues in contact with ARG 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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98A PRO 2.9 21.5 + - - +
99A ILE* 3.6 12.5 + - - +
101A SER* 1.3 73.8 + - - +
103A SER* 1.3 78.1 + - - +
105A ARG* 3.3 2.9 + - - +
106A GLN* 3.0 59.1 + - - +
113A PRO* 5.7 0.4 - - - +
118A VAL 4.8 1.4 + - - -
119A HIS* 5.2 2.2 + - - +
122A GLY* 3.3 34.1 + - - -
126A MET* 4.4 12.8 - - - +
132A LEU* 3.3 44.7 + - + +
134A TYR* 4.6 9.9 - - + -
137A LEU* 3.7 13.6 - - + +
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Residues in contact with SER 103 (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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99A ILE* 3.2 13.6 + - - +
100A LEU* 2.8 25.7 + - - -
102A ARG* 1.3 85.6 + - - +
104A LEU* 1.3 61.4 + - - -
106A GLN* 3.4 12.7 + - - +
107A MET* 3.1 22.1 + - - +
113A PRO* 3.8 19.5 - - - +
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Residues in contact with LEU 104 (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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37A PHE* 3.9 30.5 - - + -
50A ASP* 5.7 2.9 - - - +
59A MET* 4.2 17.7 - - + +
97A TYR* 5.0 4.5 - - + +
100A LEU* 3.0 22.5 + - + +
101A SER* 3.0 15.2 + - - +
103A SER* 1.3 76.5 - - - +
105A ARG* 1.3 63.4 + - + +
107A MET* 3.1 10.7 + - + +
108A ALA* 2.8 29.8 + - - +
201A FAR 3.5 48.7 - - + -
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Residues in contact with ARG 105 (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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49A ILE* 2.9 27.9 + - - +
50A ASP* 3.0 19.0 + - - +
101A SER* 2.9 25.4 + - - +
102A ARG 3.7 2.7 - - - +
104A LEU* 1.3 77.9 - - + +
106A GLN* 1.3 60.8 + - - +
108A ALA* 3.4 14.4 + - - +
109A GLN* 3.4 24.4 + - - +
134A TYR* 3.4 52.2 - - + +
136A ASP* 2.9 36.6 + - - -
137A LEU* 3.6 18.8 - - - +
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Residues in contact with GLN 106 (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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102A ARG* 3.0 61.9 + - + +
103A SER* 3.6 6.2 - - - +
105A ARG* 1.3 72.9 - - - +
107A MET* 1.3 64.6 + - - +
109A GLN* 3.1 20.8 + - - +
111A LYS* 3.1 32.9 + - + +
113A PRO* 3.3 29.3 - - + +
118A VAL* 4.3 17.6 + - + +
122A GLY* 5.0 1.4 - - - -
134A TYR* 4.8 7.9 - - + +
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Residues in contact with MET 107 (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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59A MET* 6.6 0.2 - - + -
103A SER 3.1 10.6 + - - +
104A LEU* 3.1 13.8 + - + +
106A GLN* 1.3 76.7 - - - +
108A ALA* 1.3 58.0 + - - +
110A GLY* 2.9 20.4 + - - -
111A LYS 3.3 11.8 + - - -
113A PRO* 4.2 13.6 - - + +
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Residues in contact with ALA 108 (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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55A VAL* 5.0 23.6 - - + -
104A LEU 2.8 16.7 + - - +
105A ARG* 3.5 14.4 - - - +
106A GLN 3.2 0.2 - - - -
107A MET* 1.3 73.4 - - - +
109A GLN* 1.3 58.9 + - + +
110A GLY 3.3 1.4 + - - -
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Residues in contact with GLN 109 (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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105A ARG* 3.4 15.3 + - - +
106A GLN* 3.1 13.6 + - - +
108A ALA* 1.3 76.3 - - + +
110A GLY* 1.3 56.5 + - - +
111A LYS* 2.9 17.0 + - + +
134A TYR* 3.2 29.9 + - - -
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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