Contacts of the strand formed by residues 976 - 985 (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 ILE 976 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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936B TRP* 4.2 19.7 - - + +
937B ARG* 4.5 23.8 - - + +
940B TRP* 4.2 23.8 - - + -
972B GLU* 3.7 0.9 - - - +
973B TYR* 2.8 38.8 + - - +
975B ASN* 1.3 93.9 - - + +
977B ILE* 1.3 64.1 + - - +
978B VAL* 4.0 14.7 + - + -
996B ILE* 3.9 31.0 - - + -
997B ARG 3.1 7.0 - - - +
998B ASN* 4.4 13.5 - - - +
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Residues in contact with ILE 977 (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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970B SER* 4.0 23.3 - - - +
971B GLU 3.6 10.3 - - - +
972B GLU* 4.0 25.6 - - + +
976B ILE* 1.3 76.5 - - - +
978B VAL* 1.3 63.2 + - - +
979B THR* 4.0 4.7 + - - +
995B SER 3.6 1.6 - - - +
996B ILE* 3.2 5.9 - - - -
997B ARG* 2.9 59.1 + - - +
999B THR* 3.7 26.2 - - + -
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Residues in contact with VAL 978 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
936B TRP* 3.6 42.0 - - + -
966B PRO* 3.4 15.9 - - + +
970B SER* 3.1 3.7 - - - -
971B GLU 2.9 33.5 + - - -
973B TYR* 4.0 17.3 - - + -
976B ILE* 4.0 6.5 - - + -
977B ILE* 1.3 73.9 - - - +
979B THR* 1.3 63.2 + - - +
994B PHE* 3.4 34.3 - - + -
995B SER 3.6 3.1 - - - +
996B ILE* 3.7 14.4 - - + -
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Residues in contact with THR 979 (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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969B ASN* 3.2 11.2 - - + +
970B SER* 2.6 23.0 + - - +
977B ILE* 4.4 6.6 + - - +
978B VAL* 1.3 74.1 - - - +
980B LEU* 1.3 72.8 + - - +
981B LYS* 3.4 18.6 + - + +
994B PHE* 3.3 8.2 - - - -
995B SER* 2.9 39.8 + - - -
997B ARG* 5.7 1.4 + - - -
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Residues in contact with LEU 980 (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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966B PRO* 4.0 9.8 - - - +
967B THR 3.4 26.2 - - - +
968B GLU* 4.3 3.4 - - - -
969B ASN* 2.7 27.5 + - - +
979B THR* 1.3 77.1 - - - +
981B LYS* 1.3 61.5 + - - +
982B SER* 3.7 25.4 - - - +
983B THR* 3.7 19.3 - - - +
992B ARG* 3.9 11.2 - - + +
993B ARG 3.8 4.7 - - - +
994B PHE* 3.7 31.7 - - + -
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Residues in contact with LYS 981 (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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979B THR* 3.8 31.2 - - + +
980B LEU* 1.3 74.7 - - - +
982B SER* 1.3 64.6 + - - +
993B ARG* 2.9 39.1 + - + +
994B PHE 4.3 1.6 - - - -
995B SER* 3.9 25.8 + - - +
1014B ASN* 5.4 7.5 - - - +
2051B SO4 3.1 39.9 + - - +
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Residues in contact with SER 982 (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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980B LEU* 3.7 6.1 - - - +
981B LYS* 1.3 81.7 - - - +
983B THR* 1.3 65.3 + - - +
984B LYS 4.3 0.4 + - - -
991B VAL 3.9 0.6 - - - +
992B ARG* 3.4 3.6 - - - -
993B ARG* 2.7 67.9 + - - +
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Residues in contact with THR 983 (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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980B LEU* 3.7 24.8 - - - +
982B SER* 1.3 79.2 + - - +
984B LYS* 1.3 60.6 + - - +
985B ILE* 4.2 18.1 + - + +
990B THR* 3.8 24.0 - - + -
991B VAL 3.4 4.0 - - - +
992B ARG* 4.1 12.2 + - + +
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Residues in contact with LYS 984 (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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982B SER* 4.3 0.6 + - - -
983B THR* 1.3 74.6 - - - +
985B ILE* 1.3 69.5 + - - +
986B HIS* 3.5 37.0 - - + +
990B THR* 3.5 2.9 - - - +
991B VAL* 2.8 44.5 + - + +
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Residues in contact with ILE 985 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
983B THR* 4.1 17.9 + - + +
984B LYS* 1.3 85.5 - - - +
986B HIS* 1.3 76.3 + - - +
989B TYR 4.2 1.6 - - - -
990B THR* 4.1 17.0 - - + +
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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