Contacts of the strand formed by residues 170 - 175 (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 ASP 170 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1281 THR 3.4 4.0 + - - -
1291 VAL* 3.3 15.1 - - + +
1301 GLY 3.2 21.5 + - - -
1531 ARG* 2.9 55.4 + - - +
1581 LEU* 4.3 13.2 - - - +
1591 GLY* 5.6 1.2 - - - +
1691 PHE* 1.3 81.3 - - - +
1711 LEU* 1.3 82.3 + - - +
1721 HIS* 4.2 10.4 - - - +
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Residues in contact with LEU 171 (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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1151 ILE* 4.4 23.6 - - + -
1181 MET* 3.6 35.4 - - + -
1301 GLY* 3.2 27.1 - - - +
1321 ILE* 3.9 14.1 - - + -
1491 ILE* 4.0 18.6 - - + -
1531 ARG* 2.4 35.2 + - - -
1581 LEU* 4.6 7.4 - - + +
1691 PHE* 3.4 35.4 - - + -
1701 ASP* 1.3 79.6 + - - +
1721 HIS* 1.3 65.6 + - - +
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Residues in contact with HIS 172 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1291 VAL* 4.0 24.3 - - + +
1301 GLY 3.2 5.5 + - - -
1311 TYR* 3.6 29.8 - + + -
1321 ILE* 3.4 21.2 + - - +
1531 ARG* 3.4 30.6 + - - +
1701 ASP* 4.2 9.8 - - - +
1711 LEU* 1.3 86.0 + - - +
1731 VAL* 1.3 65.1 + - - +
1741 HIS 4.0 0.2 + - - -
162 ALA 4.7 7.1 + - - -
172 LYS* 3.9 39.0 - - + +
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Residues in contact with VAL 173 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1321 ILE* 4.2 10.1 - - + +
1341 VAL* 4.8 15.7 - - + -
1421 ALA* 5.1 7.6 - - + +
1451 LEU* 4.8 14.8 - - + +
1461 GLU* 3.7 39.5 - - - +
1491 ILE* 3.6 30.3 - - + -
1531 ARG* 5.9 0.9 - - - +
1721 HIS* 1.3 75.5 - - - +
1741 HIS* 1.3 69.9 + - - +
1751 ARG* 4.3 7.0 - - + +
172 LYS* 4.5 15.2 + - - +
182 TYR* 4.0 8.8 + - - -
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Residues in contact with HIS 174 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1311 TYR* 5.4 0.9 - - + -
1321 ILE 3.1 16.0 + - - +
1331 TYR* 3.5 28.5 - + - -
1341 VAL* 3.0 30.7 + - - +
1721 HIS 5.0 1.8 - - - +
1731 VAL* 1.3 77.2 - - - +
1751 ARG* 1.3 69.8 + - - +
1921 LEU* 3.7 38.5 - - + +
182 TYR* 2.3 37.6 + + + +
252 ALA 4.5 3.1 - - - -
282 MET* 3.8 38.7 - - + +
292 PRO* 4.5 4.7 - - + +
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Residues in contact with ARG 175 (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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1341 VAL* 3.8 7.6 - - + +
1351 ARG 5.8 0.2 + - - -
1361 GLY* 4.3 11.5 + - - -
1381 TYR 4.8 1.8 + - - -
1391 ARG* 3.6 48.1 - - - +
1421 ALA* 4.0 25.7 - - + +
1731 VAL* 5.2 6.1 - - + -
1741 HIS* 1.3 87.6 + - - +
1761 GLY* 1.3 63.3 + - - +
282 MET* 4.8 12.8 - - - +
292 PRO* 5.2 9.3 - - + +
322 ARG* 2.9 60.1 + - - +
362 GLN* 4.3 9.1 + - - -
692 TYR* 4.6 2.8 + - - -
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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