Contacts of the helix formed by residues 77 - 81 (chain 1) in PDB entry 1POV
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 77 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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761 SER* 1.3 71.0 - - - +
781 GLU* 1.3 63.5 + - - +
801 PHE* 3.4 3.8 + - - +
811 PHE* 3.2 38.6 + - + -
1251 PHE* 3.9 24.9 - - + -
2661 ILE* 4.1 19.1 - - + +
2671 ARG* 5.9 0.4 - - - -
2681 VAL* 3.8 24.2 - - + +
403 VAL* 3.4 25.1 - - + +
413 LYS* 3.3 22.1 + - - +
423 ASN 4.0 4.3 - - - +
433 MET* 3.9 17.9 - - - +
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Residues in contact with GLU 78 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410 ALA* 3.2 29.9 - - - +
420 SER 5.3 7.4 - - - +
430 LYS* 4.2 15.6 - - + -
440 GLN 6.1 1.3 - - - +
761 SER* 3.3 6.9 + - - +
771 ILE* 1.3 77.7 - - - +
791 SER* 1.3 58.6 + - - +
811 PHE* 3.0 4.2 + - - +
821 ALA* 2.7 33.0 + - - +
2631 PRO 4.7 2.9 - - - +
2641 LYS* 3.4 3.9 - - - -
2651 HIS* 2.5 34.7 + - - -
2661 ILE* 2.9 27.1 + - + +
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Residues in contact with SER 79 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430 LYS* 4.4 14.8 + - - +
731 SER* 3.0 27.7 + - - -
741 GLU* 3.4 26.2 - - - +
761 SER* 3.0 8.7 + - - -
781 GLU* 1.3 76.3 - - - +
801 PHE* 1.3 62.4 + - - +
821 ALA* 3.3 20.9 + - - +
831 ARG* 4.5 3.5 + - - -
2253 LEU* 3.9 11.4 - - - +
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Residues in contact with PHE 80 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741 GLU 4.1 0.8 + - - -
761 SER 2.9 12.4 + - - +
771 ILE* 3.5 10.1 - - - +
791 SER* 1.3 78.5 - - - +
811 PHE* 1.3 78.6 + + - +
1211 LYS* 2.7 67.4 + - + -
1241 PHE* 4.5 3.4 - + - -
1251 PHE* 5.3 0.4 - + - -
433 MET* 3.8 44.6 - - + -
1033 ILE* 5.8 1.6 - - + -
1063 TYR* 3.8 35.0 - + + -
1073 TYR* 3.5 26.7 - + - +
2253 LEU* 3.6 14.9 - - + +
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Residues in contact with PHE 81 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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771 ILE* 3.2 35.8 + - + +
781 GLU 3.0 4.6 + - - +
801 PHE* 1.3 96.5 - + - +
821 ALA* 1.3 49.9 + - - +
831 ARG* 2.6 29.6 + - - +
1181 LEU* 4.1 17.4 - - + +
1211 LYS* 3.7 46.2 - - + +
1221 LEU* 3.8 26.2 - - + -
1251 PHE* 4.2 14.4 - + - -
2621 LYS* 3.9 8.1 - - - +
2631 PRO* 4.0 30.0 - - + +
2661 ILE* 3.9 18.6 - - + -
2681 VAL* 4.8 0.9 - - + -
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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