Contacts of the strand formed by residues 989 - 998 (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 TYR 989 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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986B HIS* 2.8 76.6 + + + +
987B ALA 3.7 0.4 - - - -
988B CYS* 1.3 88.1 - - + +
990B THR* 1.3 72.7 + - - +
991B VAL* 3.5 16.7 - - + +
1021B TYR* 4.0 12.1 - + - -
1022B HIS 3.2 14.1 - - - +
1023B TYR* 3.9 2.0 - - + -
1024B THR* 3.7 3.6 - - - -
1037B PRO 5.6 1.1 - - - -
1040B THR* 4.7 11.9 - - + -
1041B PHE* 3.5 44.2 - + + -
1044B ARG* 3.1 33.7 + - + +
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Residues in contact with THR 990 (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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983B THR* 3.8 23.8 - - + -
984B LYS 3.5 12.1 - - - +
985B ILE* 4.1 17.7 - - + +
986B HIS 5.1 0.2 + - - -
989B TYR* 1.3 77.2 + - - +
991B VAL* 1.3 70.8 + - - +
992B ARG* 4.0 24.1 + - + +
1020B GLN 3.4 2.3 - - - +
1021B TYR* 3.7 1.9 - - - -
1022B HIS* 2.8 43.1 + - - +
1024B THR* 4.0 13.1 + - - +
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Residues in contact with VAL 991 (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 3.9 0.3 - - - +
983B THR* 3.4 3.3 - - - -
984B LYS* 2.8 47.7 + - + +
986B HIS* 3.8 11.0 - - - +
989B TYR* 3.5 28.9 - - + +
990B THR* 1.3 72.2 - - - +
992B ARG* 1.3 65.9 + - - +
993B ARG* 4.2 3.1 + - + +
1019B ILE* 3.5 28.9 - - + -
1020B GLN 3.3 3.8 - - - +
1021B TYR* 3.8 18.8 - - + +
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Residues in contact with ARG 992 (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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965B TRP* 3.6 37.1 - - - +
980B LEU* 3.9 12.9 - - + +
982B SER 3.4 3.8 - - - -
983B THR* 4.1 14.0 + - - +
990B THR* 4.0 19.0 + - + +
991B VAL* 1.3 79.5 - - - +
993B ARG* 1.3 60.9 + - - +
994B PHE* 3.5 25.2 - - + -
1019B ILE* 3.6 1.7 - - - -
1020B GLN* 2.8 69.9 + - - +
1022B HIS* 3.1 37.0 + - - +
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Residues in contact with ARG 993 (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* 3.8 3.8 - - - +
981B LYS* 2.9 42.6 + - + +
982B SER* 2.7 55.5 + - - +
991B VAL* 4.1 3.9 + - + +
992B ARG* 1.3 72.5 - - - +
994B PHE* 1.3 62.7 + - - +
1017B VAL* 4.5 10.8 - - + -
1019B ILE* 3.3 27.6 - - + -
2051B SO4 2.6 29.3 + - - -
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Residues in contact with PHE 994 (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* 4.8 10.1 - + + -
947B ILE* 5.6 0.9 - - + -
964B TYR* 6.3 0.9 - + - -
965B TRP* 3.5 44.2 - + + -
966B PRO* 3.9 9.9 - - + -
978B VAL* 3.4 26.0 - - + -
979B THR 3.3 10.1 - - - -
980B LEU* 3.7 20.0 - - + -
981B LYS* 4.3 3.6 - - - -
992B ARG* 3.5 33.9 - - + -
993B ARG* 1.3 74.7 - - - +
995B SER* 1.3 62.5 + - - +
996B ILE* 4.7 2.2 - - + -
1017B VAL* 3.5 9.7 - - - +
1018B VAL* 2.7 50.5 + - + +
1020B GLN* 3.8 20.2 - - + -
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Residues in contact with SER 995 (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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977B ILE 3.6 1.0 - - - +
978B VAL* 3.6 0.3 - - - -
979B THR* 2.9 38.3 + - - -
981B LYS* 3.9 27.9 - - - +
994B PHE* 1.3 73.2 - - - +
996B ILE* 1.3 66.5 + - - +
1014B ASN* 3.0 36.8 + - - -
1016B ARG 3.2 6.7 - - - -
1017B VAL* 4.7 3.1 - - - +
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Residues in contact with ILE 996 (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* 3.8 14.8 - - + +
939B ILE* 4.2 16.6 - - + -
940B TRP* 3.8 27.9 - - + +
976B ILE* 3.9 14.4 - - + -
977B ILE 3.2 4.0 - - - -
978B VAL* 3.7 25.4 - - + -
994B PHE* 4.7 3.8 - - + -
995B SER* 1.3 82.2 + - - +
997B ARG* 1.3 60.8 + - - +
1015B GLU* 3.6 4.3 + - - +
1016B ARG* 2.9 46.0 + - + +
1018B VAL* 3.9 24.5 - - + -
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Residues in contact with ARG 997 (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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940B TRP* 4.4 2.9 - - - -
975B ASN 3.2 1.9 - - - +
976B ILE* 3.1 7.5 - - - -
977B ILE* 2.9 68.1 + - + +
979B THR* 5.7 1.4 + - - -
996B ILE* 1.3 74.7 - - - +
998B ASN* 1.3 71.1 + - - +
999B THR* 3.8 12.1 + - - +
1014B ASN 3.8 20.4 - - - +
1015B GLU* 4.0 19.3 - - + +
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Residues in contact with ASN 998 (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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940B TRP* 2.9 61.6 - - + +
975B ASN* 3.3 16.9 - - - +
976B ILE* 4.4 9.9 - - - +
997B ARG* 1.3 81.8 + - - +
999B THR* 1.3 64.7 + - - +
1000B LYS* 3.2 38.1 + - - +
1015B GLU* 5.0 0.2 - - - +
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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