Contacts of the strand formed by residues 1016 - 1023 (chain B) in PDB entry 3QCF
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 ARG1016 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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939B ILE 4.4 0.4 + - - -
940B TRP* 2.6 78.2 + - + +
943B ASN* 3.5 33.6 + - - +
944B THR 6.0 1.8 - - - -
995B SER* 3.2 7.8 + - - -
996B ILE* 2.9 45.4 + - + -
1014B ASN 3.0 3.0 + - - -
1015B GLU* 1.3 85.4 - - + +
1017B VAL* 1.3 67.2 + - - +
1018B VAL* 5.4 1.1 - - + -
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Residues in contact with VAL1017 (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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944B THR 4.8 0.2 - - - +
945B GLY* 3.9 13.2 - - - +
993B ARG* 4.5 9.0 - - + -
994B PHE 3.5 9.2 - - - +
995B SER* 5.6 3.1 - - - -
1014B ASN 5.2 3.8 - - - +
1016B ARG* 1.3 78.3 - - - +
1018B VAL* 1.3 68.7 + - - +
1019B ILE* 3.5 28.0 - - + -
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Residues in contact with VAL1018 (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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936B TRP* 4.6 8.3 - - + -
939B ILE* 4.2 6.7 - - + -
944B THR 3.4 23.6 - - - +
945B GLY 3.4 9.9 - - - +
947B ILE* 3.6 37.5 - - + -
994B PHE* 2.7 51.6 + - + +
995B SER* 4.9 0.2 - - - +
996B ILE* 3.9 28.7 - - + -
1016B ARG* 4.1 2.1 + - + -
1017B VAL* 1.3 77.3 - - - +
1019B ILE* 1.3 63.5 + - - +
1020B GLN 5.0 0.2 - - - +
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Residues in contact with ILE1019 (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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945B GLY 3.0 6.6 + - - +
946B ILE* 3.5 23.1 - - + +
947B ILE 2.9 25.4 + - - +
991B VAL* 3.5 29.6 - - + -
992B ARG 3.6 2.2 - - - +
993B ARG* 3.3 38.6 - - + -
1017B VAL* 3.5 20.6 - - + -
1018B VAL* 1.3 74.6 - - - +
1020B GLN* 1.3 62.6 + - - +
1021B TYR* 3.5 20.4 - - + +
1048B ALA* 6.0 0.7 - - + -
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Residues in contact with GLN1020 (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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947B ILE* 3.4 22.7 - - + +
949B MET* 3.6 17.9 - - + -
964B TYR* 3.1 26.1 + - - -
965B TRP* 3.7 15.6 - - - -
990B THR 3.4 1.6 - - - +
991B VAL* 3.3 6.4 - - - -
992B ARG* 2.8 83.4 + - - +
994B PHE* 3.8 16.9 - - + -
1018B VAL 4.0 0.6 + - - -
1019B ILE* 1.3 72.6 - - - +
1021B TYR* 1.3 71.4 + - - +
1022B HIS* 4.3 3.3 - - + +
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Residues in contact with TYR1021 (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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946B ILE* 4.1 14.1 - - + -
947B ILE 2.9 11.5 + - - +
948B VAL* 3.5 2.2 - - - -
949B MET* 2.7 32.4 + - - +
989B TYR* 4.0 16.2 - + - -
990B THR 3.7 2.0 - - - -
991B VAL* 3.8 26.2 - - + +
1019B ILE* 3.5 25.5 - - + +
1020B GLN* 1.3 75.0 - - - +
1022B HIS* 1.3 55.4 + - - +
1041B PHE* 3.5 21.4 - + + -
1044B ARG* 4.0 10.0 + - + +
1045B SER* 3.6 33.4 - - - -
1048B ALA* 3.3 33.2 - - + +
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Residues in contact with HIS1022 (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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949B MET* 3.5 30.3 - - + +
951B THR 3.0 26.9 - - - -
952B ASN* 3.6 18.8 + - - -
953B LEU* 5.6 2.2 + - - +
965B TRP* 4.6 4.3 - + - -
989B TYR* 3.2 3.5 - - - -
990B THR* 2.8 43.7 + - - +
992B ARG* 3.1 38.9 + - - +
1020B GLN* 4.3 8.7 - - - +
1021B TYR* 1.3 73.2 - - - +
1023B TYR* 1.3 66.0 + - - +
1024B THR* 3.3 13.8 - - + +
1041B PHE* 3.7 2.0 - - - -
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Residues in contact with TYR1023 (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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949B MET 3.0 14.2 + - - +
950B ILE* 4.5 4.7 - - - -
951B THR 4.0 2.4 + - - +
988B CYS* 3.7 21.6 - - + +
989B TYR* 3.9 1.8 - - + -
1022B HIS* 1.3 82.1 + - - +
1024B THR* 1.3 55.9 + - - +
1025B GLN* 3.7 30.5 + - - +
1026B TRP* 2.8 35.0 + + + +
1032B PRO* 5.0 5.9 - - + +
1034B TYR 5.1 0.9 + - - -
1037B PRO* 3.2 43.1 - - - +
1038B VAL* 3.7 18.1 - - + +
1041B PHE* 3.6 36.4 - + + -
2001B NXY 3.7 30.3 - + + -
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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