Contacts of the strand formed by residues 129 - 134 (chain 1) in PDB entry 6Q8O
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 VAL 129 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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861 GLN* 3.4 23.5 + - - +
871 HIS 3.4 1.0 - - - +
881 TYR* 3.3 33.3 - - + -
891 LEU 3.4 2.8 + - - -
1271 ALA* 3.4 2.1 - - - +
1281 THR* 1.3 86.7 + - - +
1301 GLY* 1.3 63.4 + - - +
1311 TYR* 3.9 24.0 - - + +
1691 PHE* 4.2 5.4 - - - -
1701 ASP* 3.3 19.7 - - + +
1721 HIS* 4.0 19.1 - - + +
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Residues in contact with GLY 130 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881 TYR* 4.8 0.7 - - - -
891 LEU* 3.0 19.5 - - - -
1291 VAL* 1.3 78.0 - - - +
1311 TYR* 1.3 66.3 + - - -
1691 PHE* 4.1 3.3 - - - -
1701 ASP 3.2 5.3 + - - +
1711 LEU* 3.2 23.2 - - - +
1721 HIS 3.2 22.3 + - - -
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Residues in contact with TYR 131 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881 TYR* 3.4 37.4 - + - -
891 LEU 3.1 4.1 + - - +
901 ILE* 3.2 20.7 - - + +
911 CYS 3.0 22.3 + - - -
1291 VAL* 3.9 11.0 - - + +
1301 GLY* 1.3 77.9 - - - -
1321 ILE* 1.3 62.3 + - - +
1331 TYR 4.2 0.4 - - - -
1721 HIS* 3.6 31.3 - + + -
1731 VAL 5.4 0.2 - - - -
1741 HIS* 5.4 1.8 - - + -
1921 LEU* 4.3 23.6 - - + -
2111 LEU* 4.9 7.9 - - + -
2121 TRP* 5.1 3.8 - + - -
172 LYS 2.1 34.4 + - - -
182 TYR* 3.5 35.6 - + - -
192 PRO* 3.9 8.8 - - + +
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Residues in contact with ILE 132 (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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911 CYS* 3.5 22.0 - - + -
931 ALA* 3.7 25.6 - - + -
1141 LEU* 4.1 12.6 - - + -
1151 ILE* 6.1 0.9 - - + -
1181 MET* 3.5 30.1 - - + -
1311 TYR* 1.3 79.1 - - - +
1331 TYR* 1.3 61.2 + - - +
1341 VAL* 3.6 11.3 + - + +
1451 LEU* 4.7 16.2 - - + -
1491 ILE* 5.4 5.8 - - + -
1711 LEU* 3.9 17.7 - - + -
1721 HIS 3.4 9.8 + - - +
1731 VAL* 4.2 5.8 - - + -
1741 HIS* 3.1 30.6 + - - +
1921 LEU* 5.6 0.4 - - - -
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Residues in contact with TYR 133 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901 ILE* 5.2 0.6 - - + +
911 CYS 3.1 8.9 + - - +
931 ALA* 2.9 27.9 + - - -
941 ASP* 3.0 23.5 + - + -
1311 TYR 4.2 1.0 + - - -
1321 ILE* 1.3 69.6 - - - +
1341 VAL* 1.3 65.6 + - - +
1741 HIS* 3.5 34.1 - + - -
1761 GLY* 4.1 17.7 - - - -
1771 ALA 4.4 4.3 + - - -
1781 GLY 5.4 1.0 + - - -
1791 ALA 5.4 0.2 + - - -
1821 CYS* 3.0 43.2 - - + -
1881 LEU* 3.5 45.8 - - + -
1911 SER* 3.6 21.2 + - - -
1921 LEU* 4.6 8.3 - - + -
282 MET* 4.9 1.6 - - - +
672 TYR* 4.5 3.1 - - - -
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Residues in contact with VAL 134 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
931 ALA* 3.3 24.0 - - + +
1071 LEU* 5.0 4.5 - - + -
1321 ILE* 3.8 15.5 - - + +
1331 TYR* 1.3 77.2 - - - +
1351 ARG* 1.3 65.7 + - - +
1381 TYR* 4.6 14.6 - - + +
1411 ALA* 6.3 1.1 - - + -
1421 ALA* 4.6 7.9 - - + +
1451 LEU* 4.1 18.8 - - + -
1731 VAL* 4.8 7.6 - - + -
1741 HIS 3.0 19.8 + - - +
1751 ARG* 3.9 17.9 - - + +
1761 GLY* 2.8 27.7 + - - -
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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
------------------------------------------------------------
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