Contacts of the helix formed by residues 98 - 105 (chain B) in PDB entry 3V5I
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 ALA 98 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B PRO 4.1 9.6 - - - +
68B GLY* 4.4 2.9 - - - -
69B GLY 5.1 2.9 - - - +
97B ALA* 1.3 74.0 - - + +
99B MET* 1.3 67.7 + - - +
101B SER* 2.8 23.5 + - - -
102B PHE* 3.1 6.0 + - - +
121B MET* 3.0 14.0 + - + -
122B ILE* 5.0 0.4 - - - +
123B HIS* 3.2 42.2 + - + +
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Residues in contact with MET 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ILE* 4.1 9.0 - - + -
68B GLY* 4.1 0.6 - - - -
69B GLY 4.1 22.4 - - - +
70B SER 4.1 7.0 - - - +
71B VAL* 3.7 34.1 - - + +
74B GLY* 3.7 32.3 - - - -
75B PHE* 4.9 1.1 - - - -
98B ALA* 1.3 79.3 - - - +
100B GLY* 1.3 60.5 + - - +
102B PHE* 3.3 31.3 + - + +
103B LEU* 3.1 24.3 + - + +
150B LEU* 3.7 25.6 - - + -
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Residues in contact with GLY 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ILE* 4.0 12.5 - - - +
64B ILE* 4.2 8.0 - - - +
66B SER* 4.4 13.2 - - - -
68B GLY* 3.8 4.0 - - - -
96B ALA* 4.0 7.7 - - - +
97B ALA 2.7 23.0 + - - -
99B MET* 1.3 71.1 - - - +
101B SER* 1.3 55.4 + - - -
103B LEU* 3.2 7.5 + - - +
104B LEU* 3.0 25.1 + - - +
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Residues in contact with SER 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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96B ALA* 3.2 24.8 - - - -
97B ALA 3.5 3.0 + - - -
98B ALA 2.8 18.3 + - - -
100B GLY* 1.3 72.2 - - - +
102B PHE* 1.3 65.9 + - - +
104B LEU* 3.2 10.6 + - - +
105B ALA* 3.1 23.9 + - - +
120B VAL* 3.6 17.5 - - - -
121B MET 3.1 17.3 + - - -
122B ILE* 3.4 14.9 - - - +
185B LEU* 4.6 5.7 - - - +
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Residues in contact with PHE 102 (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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75B PHE* 3.7 34.5 - + - -
78B TYR* 3.6 26.2 - + + -
98B ALA 3.1 3.6 + - - +
99B MET* 3.3 36.1 - - + +
101B SER* 1.3 83.3 + - - +
103B LEU* 1.3 67.5 + - + +
105B ALA* 3.4 5.4 + - - +
106B ALA* 3.3 18.7 + - - +
150B LEU* 3.7 34.5 - - + -
153B ILE* 3.8 25.6 - - + -
154B LEU* 4.0 28.7 - - + +
157B ARG* 5.7 0.6 - - - -
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Residues in contact with LEU 103 (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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32B LEU* 4.2 11.4 - - + -
36B ILE* 3.9 26.2 - - + -
62B LEU* 5.5 2.0 - - + -
64B ILE* 4.0 11.2 - - + -
74B GLY* 3.5 26.2 - - - +
77B ILE* 4.0 31.2 - - + -
78B TYR* 3.8 24.5 - - + +
81B ILE* 4.9 7.6 - - + +
90B THR* 3.7 8.0 - - - +
99B MET* 3.1 16.0 + - + +
100B GLY 3.2 6.9 + - - +
102B PHE* 1.3 78.9 - - + +
104B LEU* 1.3 68.0 + - - +
106B ALA* 2.9 18.0 + - - +
107B GLY 3.6 3.5 + - - -
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Residues in contact with LEU 104 (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 ILE* 3.7 12.0 - - + +
90B THR* 2.6 37.7 + - - +
91B ILE 4.3 0.4 - - - -
92B CYS* 3.6 30.7 - - + +
96B ALA* 4.2 7.2 - - + -
100B GLY 3.0 13.1 + - - +
101B SER* 3.2 11.2 + - - +
103B LEU* 1.3 76.4 - - - +
105B ALA* 1.3 58.4 - - - +
106B ALA 3.2 2.6 + - - -
107B GLY 3.4 1.6 + - - -
112B ARG* 3.6 5.9 - - - +
113B PHE 3.5 22.7 - - - +
114B ALA* 5.3 0.2 - - + -
120B VAL* 3.8 25.6 - - + -
185B LEU* 4.3 5.4 - - + +
186B ILE* 3.7 24.9 - - + -
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Residues in contact with ALA 105 (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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101B SER 3.1 12.1 + - - +
102B PHE 3.7 5.6 - - - +
103B LEU 3.2 0.2 - - - -
104B LEU* 1.3 77.4 - - - +
106B ALA* 1.3 57.9 + - - +
107B GLY 3.4 0.7 - - - -
112B ARG* 2.9 26.7 + - - +
154B LEU* 4.3 12.6 - - + -
157B ARG* 3.5 19.7 + - + -
158B THR* 5.0 1.1 - - + -
185B LEU* 3.4 41.5 - - + +
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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