Contacts of the strand formed by residues 1211 - 1214 (chain B) in PDB entry 1Q6S
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 VAL1211 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1080B SER 4.1 3.2 + - - +
1081B TYR* 3.7 26.0 - - + -
1082B ILE 2.9 25.3 + - - +
1104B SER* 4.7 1.6 - - - +
1106B GLY* 3.4 24.2 - - - +
1108B VAL* 3.8 27.8 - - + -
1174B PHE* 6.2 0.2 - - + -
1198B VAL* 5.1 0.2 - - + -
1203B SER* 4.3 11.9 + - - +
1204B LEU* 3.3 34.2 - - + +
1209B GLY 3.5 2.6 + - - -
1210B PRO* 1.3 72.7 - - - +
1212B VAL* 1.3 63.4 + - - +
1213B VAL* 3.8 7.8 + - + -
1225B PHE* 5.6 0.7 - - + -
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Residues in contact with VAL1212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1082B ILE* 3.5 18.4 - - + +
1084B THR* 3.8 17.0 - - + -
1095B PHE* 3.8 29.8 - - + -
1098B MET* 4.0 12.8 - - + -
1099B VAL* 4.0 15.9 - - + -
1104B SER* 3.5 26.0 - - - +
1106B GLY 3.1 10.1 + - - +
1107B VAL* 3.1 10.2 - - + +
1108B VAL 2.7 32.7 + - - +
1210B PRO 4.1 0.9 - - - +
1211B VAL* 1.3 71.5 - - - +
1213B VAL* 1.3 56.8 + - - +
1214B HIS* 5.2 0.2 - - + -
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Residues in contact with VAL1213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1081B TYR* 4.5 1.3 - - + -
1082B ILE 2.8 12.3 + - - +
1083B LEU* 3.3 5.9 - - + -
1084B THR* 3.0 24.4 + - - +
1108B VAL* 3.4 18.6 - - + +
1110B LEU* 4.0 7.6 - - + -
1211B VAL* 3.9 23.1 - - + +
1212B VAL* 1.3 75.3 - - - +
1214B HIS* 1.3 64.8 + - - +
1222B SER* 3.7 24.5 + - - +
1225B PHE* 3.9 24.5 - - + -
1226B CYS* 3.9 22.2 - - - -
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Residues in contact with HIS1214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1084B THR* 3.0 33.9 - - + +
1085B GLN 4.0 4.9 - - - +
1086B GLY* 3.5 11.0 - - - -
1087B PRO* 4.6 0.2 - - + -
1095B PHE* 4.3 9.9 - + - -
1107B VAL* 4.1 11.0 - - + -
1108B VAL 2.9 17.0 + - - +
1109B MET* 3.5 19.1 - - + +
1110B LEU* 2.9 25.6 + - - +
1111B ASN* 3.2 20.4 - - - -
1121B CYS* 4.2 0.9 - - - -
1124B TYR* 2.6 40.4 + + - -
1212B VAL* 5.3 0.4 - - + -
1213B VAL* 1.3 75.4 - - - +
1215B CYS* 1.3 76.5 + - - +
1222B SER* 3.2 8.8 + - - -
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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