Contacts of the strand formed by residues 87 - 93 (chain 1) in PDB entry 6Q8W
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 HIS 87 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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791 MET* 3.6 17.2 - - + +
801 PRO* 4.8 0.7 - - + -
811 LYS* 4.3 20.2 - - - -
821 ASP* 4.9 1.6 - - - -
831 ASP* 2.7 38.6 + - - -
851 LYS 3.2 12.2 + - - -
861 GLN* 1.3 99.2 + - - +
881 TYR* 1.3 66.2 + - - +
1251 ILE* 3.1 24.4 + - + +
1261 ARG* 3.9 22.2 + - + +
1271 ALA* 4.4 5.4 - - + -
1281 THR 3.9 4.2 + - - -
1291 VAL 3.6 7.8 - - - +
2151 PRO* 3.5 29.3 - - + +
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Residues in contact with TYR 88 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
861 GLN* 3.9 27.6 + - + +
871 HIS* 1.3 76.3 - - - +
891 LEU* 1.3 61.5 + - - +
901 ILE* 5.1 3.8 - - + -
1251 ILE* 4.7 2.7 - - - +
1271 ALA* 4.4 3.4 - - - -
1291 VAL* 3.5 17.9 - - + -
1311 TYR* 3.9 34.3 - + + -
2111 LEU* 4.2 14.8 - - + -
2121 TRP* 4.7 8.6 - + + +
2141 LYS* 3.7 37.9 + - + +
2151 PRO 4.0 4.4 + - - +
2161 THR* 3.2 23.0 - - + +
2171 THR* 3.1 26.2 + - - -
192 PRO* 3.6 25.6 - - + +
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Residues in contact with LEU 89 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881 TYR* 1.3 74.8 - - - +
901 ILE* 1.3 68.5 + - - +
1181 MET* 3.5 46.0 - - + +
1211 ALA* 3.6 20.0 - - + -
1221 GLY* 3.9 5.6 - - - +
1251 ILE* 3.9 14.4 - - + -
1271 ALA* 3.8 16.7 - - + +
1291 VAL 3.5 5.9 + - - -
1301 GLY* 3.1 7.6 - - - -
1311 TYR 2.8 27.2 + - - +
1691 PHE* 4.5 4.0 - - + -
2171 THR* 3.2 20.2 - - - +
2191 ASN* 4.3 15.5 - - - +
2241 LEU* 4.6 5.6 - - + -
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Residues in contact with ILE 90 (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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881 TYR* 5.0 2.7 - - + +
891 LEU* 1.3 84.2 - - - +
911 CYS* 1.3 73.0 + - - +
921 ASN* 4.4 0.9 - - - +
1311 TYR* 3.3 13.5 - - + +
1331 TYR* 5.3 0.9 - - + -
1881 LEU* 4.2 23.8 - - + -
1891 MET* 4.2 13.7 - - + -
1921 LEU* 5.7 1.1 - - + -
2111 LEU* 3.9 27.8 - - + -
2161 THR* 4.5 12.8 - - - +
2171 THR 2.9 7.4 + - - +
2181 ILE* 3.5 41.7 - - + -
2191 ASN* 3.2 26.3 + - - +
2241 LEU* 4.7 0.7 - - - +
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Residues in contact with CYS 91 (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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901 ILE* 1.3 76.1 - - - +
921 ASN* 1.3 58.7 + - - +
931 ALA* 3.2 4.4 + - - -
1141 LEU* 3.9 18.2 - - - -
1181 MET* 3.7 22.0 - - + +
1311 TYR 2.8 8.3 + - - -
1321 ILE* 3.7 27.8 - - + -
1331 TYR* 3.1 24.6 + - - +
2211 VAL* 3.6 27.1 - - - -
2241 LEU* 3.8 19.7 - - + -
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Residues in contact with ASN 92 (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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661 GLY* 6.3 0.4 - - - -
901 ILE* 3.7 0.6 + - - -
911 CYS* 1.3 69.8 - - - +
931 ALA* 1.3 56.7 + - - +
941 ASP* 3.4 14.6 + - - +
1031 ASP* 5.1 1.2 - - - +
1831 GLY* 3.6 18.7 + - - +
1851 GLU* 5.1 4.4 - - - +
1881 LEU* 3.1 28.9 - - - +
2181 ILE* 3.7 22.1 - - + +
2191 ASN 3.3 22.4 + - - +
2201 ASN* 4.8 11.0 + - - +
2211 VAL* 3.3 17.0 + - - +
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Residues in contact with ALA 93 (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* 3.2 1.9 + - - +
921 ASN* 1.3 72.5 - - - +
941 ASP* 1.3 60.0 + - - +
951 GLU* 3.2 10.8 + - - +
1031 ASP* 6.3 0.7 - - - -
1071 LEU* 4.1 19.6 - - + +
1321 ILE* 4.2 10.8 - - + -
1331 TYR 3.0 21.4 + - - +
1341 VAL* 3.6 24.3 - - + +
1351 ARG* 3.8 13.5 + - - +
1381 TYR* 5.1 1.2 - - - -
2211 VAL* 3.9 13.2 - - + -
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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