Contacts of the helix formed by residues 56 - 64 (chain H) in PDB entry 2VIG
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 ILE 56 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52H GLU 3.6 12.8 - - - +
53H LEU* 3.1 22.1 + - + +
55H PRO* 1.3 81.8 - - + +
57H ALA* 1.3 66.4 + - - +
58H ALA 3.3 2.2 - - - -
59H GLN* 3.1 12.9 + - - +
60H VAL* 2.9 40.2 + - + +
67H PRO* 4.0 7.9 - - + -
70H GLN* 3.5 42.4 - - + +
109H CYS* 5.4 2.5 - - - -
112H THR* 5.1 1.1 - - - +
502H EDO 3.8 26.5 - - - +
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Residues in contact with ALA 57 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53H LEU 3.0 8.6 + - - +
54H PHE* 3.5 11.6 + - + +
56H ILE* 1.3 79.5 - - - +
58H ALA* 1.3 62.0 + - - +
60H VAL* 3.5 6.8 + - - +
61H ASP* 3.2 23.7 + - - +
108H GLY 3.5 24.7 - - - +
109H CYS* 4.6 10.7 - - + -
380H ARG* 3.6 30.0 - - - +
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Residues in contact with ALA 58 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54H PHE 4.8 1.4 + - - -
55H PRO 5.2 1.7 + - - +
56H ILE 3.3 0.6 - - - -
57H ALA* 1.3 76.2 - - - +
59H GLN* 1.3 53.6 + - - +
61H ASP* 3.4 5.8 + - - +
62H LYS* 2.8 36.8 + - - +
374H THR 6.1 1.3 - - - +
380H ARG* 4.4 15.5 - - - +
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Residues in contact with GLN 59 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55H PRO 5.6 1.5 + - - +
56H ILE* 3.1 16.7 + - - +
58H ALA* 1.3 77.6 - - - +
60H VAL* 1.3 59.8 + - - +
62H LYS* 4.3 6.7 - - - +
63H GLU* 2.8 62.8 + - - +
65H LEU* 3.6 13.5 - - + +
502H EDO 3.4 25.6 + - - -
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Residues in contact with VAL 60 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56H ILE* 2.9 45.1 + - + +
57H ALA* 3.8 5.2 - - - +
59H GLN* 1.3 75.9 - - - +
61H ASP* 1.3 56.5 + - - +
64H HIS* 3.1 9.2 + - - -
65H LEU* 3.0 50.3 + - - +
67H PRO* 4.3 8.1 - - + -
109H CYS* 4.2 20.2 - - - -
111H SER* 4.2 4.9 - - - +
235H GLY* 3.6 20.6 + - - +
502H EDO 4.1 15.3 - - - -
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Residues in contact with ASP 61 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57H ALA 3.2 17.0 + - - +
58H ALA* 3.6 4.9 - - - +
59H GLN 3.2 0.2 - - - -
60H VAL* 1.3 77.5 - - - +
62H LYS* 1.3 68.3 + - - +
63H GLU 3.5 0.2 + - - -
64H HIS 3.7 3.5 + - - -
234H ARG* 3.1 50.4 + - - +
235H GLY 5.3 0.7 - - - +
374H THR* 5.9 1.0 - - - +
379H GLU* 4.8 0.2 - - - +
380H ARG* 3.6 21.7 - - - +
383H ARG* 2.9 45.5 + - - -
384H ASP* 4.6 4.9 - - - +
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Residues in contact with LYS 62 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229G ASP* 4.6 14.3 + - - -
58H ALA 2.8 21.7 + - - +
59H GLN* 3.3 6.7 + - - +
61H ASP* 1.3 79.5 - - - +
63H GLU* 1.3 72.1 + - + +
64H HIS* 3.5 12.8 + - - -
234H ARG* 4.9 5.4 + - - +
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Residues in contact with GLU 63 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59H GLN* 2.8 46.8 + - + +
62H LYS* 1.3 91.0 - - + +
64H HIS* 1.3 74.8 + - - +
65H LEU* 3.2 18.2 + - + +
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Residues in contact with HIS 64 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60H VAL 3.1 8.1 + - - -
61H ASP 3.7 3.8 + - - -
62H LYS 3.5 16.8 + - - -
63H GLU* 1.3 79.5 - - - +
65H LEU* 1.3 59.4 + - - +
66H PHE 4.0 2.1 + - - -
227H LYS* 5.0 9.9 + - - +
228H GLU 5.1 3.4 + - - -
229H ASP* 3.3 29.5 + - - -
230H LYS* 4.4 6.5 + - - -
234H ARG* 3.2 61.9 + - + +
235H GLY 5.2 0.2 - - - +
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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