Contacts of the helix formed by residues 62 - 69 (chain B) in PDB entry 5V2C
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 62 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B TRP* 3.6 36.3 - - + -
34B ALA* 4.7 5.2 - - + +
37B MET* 3.9 6.7 - - + -
38B ALA* 3.7 31.6 - - + +
41B GLU* 3.0 25.9 + - - +
61B PHE* 1.3 80.6 - - + +
63B LEU* 1.3 66.3 + - - +
64B PRO* 3.3 2.5 - - - -
65B PHE* 2.9 22.4 + - + +
66B MET* 3.1 21.4 + - + +
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Residues in contact with LEU 63 (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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38B ALA 5.7 0.2 - - - +
41B GLU* 2.8 27.9 + - + +
42B LEU* 4.5 13.7 - - + -
45B PHE* 3.8 48.7 - - + -
55B MET* 4.0 17.9 - - + -
60B MET* 3.9 8.5 - - + -
62B VAL* 1.3 72.9 - - - +
64B PRO* 1.4 63.9 - - + +
66B MET* 3.1 15.6 + - + +
67B ALA* 2.9 27.9 + - - +
78B TRP* 5.2 0.2 - - + -
80B ILE* 4.6 3.1 - - + -
93B PHE* 3.7 37.0 - - + -
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Residues in contact with PRO 64 (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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55B MET* 3.6 14.8 - - - -
60B MET 3.8 15.3 - - - +
61B PHE* 3.3 23.3 - - - +
62B VAL 3.4 1.6 - - - -
63B LEU* 1.4 94.3 - - + +
65B PHE* 1.3 51.4 + - - +
67B ALA* 3.4 2.9 + - + -
68B ARG* 2.7 35.2 + - - +
267B LEU* 3.4 38.3 - - + +
268B PHE* 3.7 24.0 - - + -
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Residues in contact with PHE 65 (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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61B PHE* 3.1 36.8 - + - -
62B VAL* 2.9 14.3 + - + +
64B PRO* 1.3 73.6 - - - +
66B MET* 1.3 66.8 + - + +
68B ARG* 3.4 49.2 + - - +
69B LEU* 3.7 16.8 + - - +
256B MET* 4.5 2.9 - - + -
268B PHE* 3.7 28.0 - + - -
451B PHE* 3.8 34.3 - + - -
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Residues in contact with MET 66 (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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38B ALA* 4.0 25.6 - - + +
62B VAL* 3.1 24.7 + - + +
63B LEU* 3.1 21.7 + - + +
65B PHE* 1.3 78.3 - - + +
67B ALA* 1.3 61.8 - - - +
69B LEU* 3.4 7.1 + - - +
70B GLY 3.4 0.5 + - - -
71B VAL* 2.9 33.7 + - + +
93B PHE* 3.7 41.3 - - + +
96B VAL* 3.6 38.4 - - + -
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Residues in contact with ALA 67 (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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55B MET* 4.2 3.8 - - + -
63B LEU 2.9 15.8 + - - +
64B PRO 3.7 3.6 - - - +
66B MET* 1.3 75.0 - - - +
68B ARG* 1.3 66.1 + - - +
69B LEU 3.1 0.9 + - - -
70B GLY 3.1 9.0 + - - -
71B VAL 3.1 14.9 + - - +
72B THR* 4.7 0.4 - - - -
80B ILE* 3.7 29.2 - - + -
93B PHE* 4.9 1.3 - - + -
167B TRP* 4.1 4.7 - - + -
178B VAL* 3.6 15.9 - - - +
267B LEU* 3.9 15.5 - - + -
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Residues in contact with ARG 68 (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 PRO 2.7 21.3 + - - +
65B PHE* 3.4 42.1 + - - +
66B MET 3.3 0.6 - - - -
67B ALA* 1.3 73.4 - - - +
69B LEU* 1.3 75.8 + - + +
166B MET* 3.3 14.5 - - + +
167B TRP* 2.9 31.5 + - + +
256B MET* 5.8 0.6 - - - +
262B THR* 2.9 50.4 + - - +
263B THR* 4.8 4.4 - - - +
264B PRO* 4.8 5.2 - - + -
267B LEU* 3.7 13.7 - - + +
268B PHE* 5.0 5.2 - - - -
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Residues in contact with LEU 69 (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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65B PHE 3.7 13.6 + - - +
66B MET* 3.4 4.4 + - - +
67B ALA 3.1 0.8 - - - -
68B ARG* 1.3 100.5 - - + +
70B GLY* 1.3 57.8 + - - +
71B VAL* 3.7 4.3 - - + +
153B PHE* 3.7 36.3 - - + -
157B HIS* 2.8 36.2 + - + +
158B LEU* 4.4 11.4 - - + -
164B PRO* 3.2 6.4 - - - +
165B GLY 4.0 5.2 - - - -
166B MET* 5.0 1.1 - - + -
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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