Contacts of the helix formed by residues 51 - 55 (chain V) in PDB entry 3H1I
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 CYS 51 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133N VAL* 4.6 9.0 - - + -
136N GLN* 4.1 21.5 - - + -
137N GLU* 4.3 13.5 - - - -
140N GLU* 3.4 17.0 - - - -
306O PRO* 3.5 12.6 - - + -
50V LEU* 1.3 79.3 - - - +
52V ARG* 1.3 67.7 + - - +
53V GLU* 3.2 13.2 - - - +
54V SER* 3.2 30.2 + - - -
55V MET* 3.4 14.2 - - - +
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Residues in contact with ARG 52 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129N LYS* 6.0 4.4 - - - +
296O TYR* 4.2 19.3 - - - +
300O ALA* 4.7 9.6 + - - +
303O THR 3.8 10.1 + - - -
304O THR 3.3 17.0 + - - -
305O GLN 3.2 23.0 + - - -
306O PRO* 3.3 14.7 - - + +
307O PHE* 2.9 58.5 - - - +
51V CYS* 1.3 71.3 - - - +
53V GLU* 1.3 74.0 + - - +
55V MET* 2.9 13.8 + - - -
56V SER* 3.0 17.8 + - - -
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Residues in contact with GLU 53 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65N LYS* 4.9 2.2 + - - +
129N LYS* 5.6 5.9 + - - -
130N GLU* 5.0 7.7 - - - +
133N VAL* 3.4 34.0 - - + +
137N GLU* 4.2 14.4 - - - +
287O ARG* 3.4 57.9 + - + +
288O GLY 3.9 7.3 - - - +
51V CYS* 3.2 9.3 + - - +
52V ARG* 1.3 88.2 + - - +
54V SER* 1.3 57.7 + - - +
56V SER* 3.3 17.0 + - - +
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Residues in contact with SER 54 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137N GLU* 4.4 12.5 + - - +
140N GLU* 3.4 27.2 + - - -
49V LEU* 2.9 26.3 - - - +
51V CYS* 3.2 19.8 + - - -
53V GLU* 1.3 75.7 - - - +
55V MET* 1.3 59.2 + - - +
56V SER 5.1 1.1 - - - -
58V ARG* 4.1 11.5 - - - +
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Residues in contact with MET 55 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252O LEU* 4.8 9.9 - - + -
306O PRO* 4.3 5.8 - - - -
307O PHE* 3.5 31.4 - - - +
308O ASP* 3.3 9.9 - - + +
327O ILE* 3.4 52.6 - - + +
328O SER* 4.4 3.6 - - - +
49V LEU* 4.1 25.1 - - + -
50V LEU* 4.9 2.7 - - - -
51V CYS 3.4 23.1 - - - +
52V ARG 2.9 6.0 + - - +
54V SER* 1.3 80.2 - - - +
56V SER* 1.3 68.2 + - - +
58V ARG* 3.1 27.0 + - - +
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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