Contacts of the strand formed by residues 319 - 325 (chain 0) 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 THR 319 (chain 0).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1340 THR* 3.7 29.6 - - + -
1350 LEU 4.3 2.2 - - - +
1370 THR* 2.8 31.9 + - - +
1790 VAL* 3.8 0.2 - - - -
1800 GLN* 2.8 66.3 + - - +
3170 PRO* 4.1 2.0 - - - +
3180 ILE* 1.3 72.3 - - - +
3200 LEU* 1.3 62.4 + - - +
3210 THR* 4.5 0.2 - - - +
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Residues in contact with LEU 320 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1340 THR* 3.6 1.6 - - - +
1350 LEU* 2.9 44.8 + - + +
1360 ASP 5.4 2.6 + - - +
1490 TRP* 3.5 55.9 - - + +
1770 VAL* 4.3 13.0 - - + -
1780 HIS 3.9 0.4 - - - +
1790 VAL* 3.4 41.3 - - + -
2980 ILE* 4.9 5.8 - - + -
3000 ILE* 4.1 6.5 - - + -
3180 ILE* 4.1 4.3 + - + +
3190 THR* 1.3 75.0 - - - +
3210 THR* 1.3 61.3 + - - +
3220 ILE* 4.6 14.6 - - + -
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Residues in contact with THR 321 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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920 ILE* 5.3 5.4 - - + -
1320 PHE* 3.7 32.3 - - + -
1330 TYR 3.5 8.3 - - - +
1340 THR* 2.7 29.1 + - - +
1760 THR 3.7 1.7 - - - +
1780 HIS* 2.9 45.5 + - + +
1800 GLN* 2.9 24.9 + - - -
3200 LEU* 1.3 72.7 - - - +
3220 ILE* 1.3 62.2 + - - +
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Residues in contact with ILE 322 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1310 ARG 3.6 1.2 - - - +
1320 PHE* 4.1 1.8 - - - -
1330 TYR* 2.8 43.5 + - - +
1350 LEU* 4.2 25.8 - - + -
1490 TRP* 6.0 2.5 - - + -
1510 LEU* 4.2 19.7 - - + -
1540 ALA* 5.2 1.6 - - + -
1550 LEU* 4.2 16.2 - - + +
1750 TYR* 4.2 23.3 - - + -
1760 THR 3.4 8.3 - - - +
1770 VAL* 4.1 28.3 - - + -
2980 ILE* 5.3 4.0 - - + -
3200 LEU* 4.0 14.6 + - + -
3210 THR* 1.3 79.7 - - - +
3230 ALA* 1.3 65.3 + - - +
3240 PRO* 4.0 0.5 - - - +
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Residues in contact with ALA 323 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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870 LEU* 4.7 6.7 - - + -
1310 ARG* 3.2 19.5 - - - +
1320 PHE* 3.3 33.0 - - + -
1750 TYR* 3.3 1.6 - - - -
1760 THR* 2.8 40.7 + - - +
3220 ILE* 1.3 77.3 - - - +
3240 PRO* 1.3 69.3 - - - +
3250 MET* 3.8 2.2 - - + +
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Residues in contact with PRO 324 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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870 LEU* 5.2 2.1 - - - +
1300 CYS* 3.5 43.4 - - - +
1310 ARG 3.2 15.7 - - - +
1330 TYR* 4.1 3.6 - - + -
1550 LEU* 3.9 21.3 - - + -
1610 PHE* 3.6 32.8 - - + -
1730 SER* 3.4 14.6 - - - +
1740 GLY 3.3 7.0 - - - +
1750 TYR* 4.0 5.1 - - + -
3220 ILE 4.0 1.1 - - - +
3230 ALA* 1.3 87.5 - - - +
3250 MET* 1.3 61.2 + - - +
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Residues in contact with MET 325 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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870 LEU* 5.1 22.2 - - + -
1070 TRP* 3.9 24.7 - - + +
1080 PRO* 3.8 30.5 - - + -
1300 CYS* 5.6 0.2 - - - -
1740 GLY* 2.7 39.7 + - - +
1750 TYR 4.1 1.6 - - - +
1760 THR* 2.9 33.2 - - - +
2780 VAL* 4.7 1.8 - - - -
3230 ALA* 3.8 11.4 - - + +
3240 PRO* 1.3 80.1 - - - +
3260 CYS* 1.4 77.4 + - - +
3270 CYS* 2.9 5.9 + - - -
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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