Contacts of the helix formed by residues 99 - 106 (chain 3) 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 MET 99 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2580 ASN* 2.9 13.8 + - - +
2610 VAL* 3.9 24.0 - - + -
1241 PHE* 3.6 22.4 - - + -
2721 ARG 3.5 23.1 - - - +
2731 PRO* 4.2 2.2 - - - -
2741 PRO* 3.5 24.2 - - - -
463 LEU* 3.8 38.1 - - + +
493 ILE 4.9 1.6 - - - +
513 THR* 3.1 27.9 + - + -
983 THR* 1.3 68.9 - - - +
1003 LEU* 1.3 63.9 + - - +
1023 GLU* 3.3 3.6 + - - +
1033 ILE* 3.1 32.5 + - + +
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Residues in contact with LEU 100 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473 ALA* 3.9 37.3 + - + +
493 ILE 5.5 1.4 + - - +
513 THR* 4.5 1.6 + - - -
893 PRO* 4.4 11.9 - - + +
953 LEU* 6.2 1.8 - - + -
983 THR* 3.2 6.8 + - - +
993 MET* 1.3 78.2 - - - +
1013 GLY* 1.3 62.5 + - - +
1033 ILE* 3.4 2.1 + - - +
1043 LEU* 2.9 36.7 + - + +
1143 LEU* 3.4 29.6 - - + -
2143 VAL* 4.2 23.1 - - + +
2153 SER* 4.5 6.7 - - - -
2163 ALA* 4.0 16.6 - - + -
2203 PHE* 4.1 17.5 - - + -
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Residues in contact with GLY 101 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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893 PRO 3.5 24.5 - - - -
953 LEU 3.7 4.0 - - - -
963 SER* 3.4 13.7 - - - -
983 THR* 3.0 10.6 + - - -
1003 LEU* 1.3 78.9 - - - +
1023 GLU* 1.3 62.0 + - - +
1043 LEU* 3.2 6.0 + - - +
1053 ASN* 2.9 28.6 + - - -
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Residues in contact with GLU 102 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2550 LEU* 5.8 0.2 - - - +
2580 ASN* 4.9 1.1 - - - +
1201 ARG* 2.9 35.7 + - - -
1241 PHE* 4.9 2.5 - - + -
2741 PRO* 3.7 26.7 - - + -
2761 ALA* 5.9 2.1 - - - +
963 SER 3.5 1.1 + - - -
973 HIS* 2.7 43.4 + - - +
983 THR 2.8 22.6 + - - +
993 MET 3.6 4.7 - - - +
1013 GLY* 1.3 72.4 - - - +
1033 ILE* 1.3 61.6 + - - +
1053 ASN* 3.2 17.3 + - - +
1063 TYR* 3.5 14.7 - - - -
2283 THR* 5.0 0.5 + - - -
2303 HIS* 2.8 19.4 + - - +
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Residues in contact with ILE 103 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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801 PHE* 6.1 0.7 - - + -
1241 PHE* 4.2 16.6 - - + -
433 MET* 3.6 26.0 - - + +
443 MET* 3.7 28.9 - - + -
463 LEU* 3.6 34.5 - - + -
473 ALA* 3.6 12.3 - - + +
993 MET* 3.1 25.9 + - + +
1003 LEU 3.8 3.6 - - - +
1023 GLU* 1.3 75.1 - - - +
1043 LEU* 1.3 64.4 + - + +
1063 TYR* 3.0 19.8 + - + +
1073 TYR* 3.6 18.3 - - + -
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Residues in contact with LEU 104 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443 MET* 5.3 2.2 - - + -
893 PRO* 3.5 37.9 - - + -
903 ALA* 3.9 16.6 - - + +
1003 LEU* 2.9 28.8 + - + +
1013 GLY 3.4 9.4 - - - +
1033 ILE* 1.3 77.5 - - + +
1053 ASN* 1.3 57.0 + - - +
1073 TYR* 2.9 27.7 + - - +
1103 TRP* 3.8 19.1 - - + -
1793 THR* 3.3 12.4 - - + +
2203 PHE* 3.8 13.7 - - + -
2223 VAL* 3.5 30.7 - - + -
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Residues in contact with ASN 105 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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903 ALA* 3.2 31.0 + - - +
963 SER 4.0 1.0 + - - -
1013 GLY 2.9 26.7 + - - -
1023 GLU* 3.5 11.2 - - - +
1033 ILE 3.1 1.0 + - - -
1043 LEU* 1.3 74.9 - - - +
1063 TYR* 1.3 55.9 + - - +
1073 TYR 3.1 5.4 - - - -
1793 THR 4.6 1.6 - - - +
2263 ARG* 3.2 39.8 + - - +
2273 ASP 3.9 0.5 - - - +
2283 THR* 3.5 25.0 + - - +
2293 THR* 4.6 4.2 + - - -
2303 HIS* 3.7 27.3 + - + -
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Residues in contact with TYR 106 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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801 PHE* 3.8 24.0 - + + -
1171 GLN* 4.9 1.5 + - + -
1201 ARG* 3.1 51.1 + - - +
1211 LYS* 3.7 34.7 + - + +
1241 PHE* 3.6 26.6 - + - -
1023 GLU 3.5 18.4 - - - -
1033 ILE* 3.0 12.2 + - - +
1053 ASN* 1.3 78.0 - - - +
1073 TYR* 1.3 56.2 + - + +
2253 LEU* 3.2 11.5 - - + +
2263 ARG* 2.7 44.9 + - - +
2273 ASP* 4.8 5.4 - - - -
2283 THR* 3.5 24.7 - - + +
2313 ILE* 4.8 0.7 - - - +
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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