Contacts of the strand formed by residues 1029 - 1035 (chain B) in PDB entry 3F5P
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 ARG1029 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1015B GLU* 2.5 35.7 + - - +
1016B GLY 3.4 9.0 - - - +
1017B VAL* 5.6 5.4 - - + -
1028B THR* 1.3 84.8 - - - +
1030B VAL* 1.3 67.6 + - - +
1080B GLU* 4.8 0.2 - - - -
1081B LEU* 3.6 29.8 + - + +
1083B THR* 3.9 24.1 - - - +
1145B GLU* 4.9 7.5 + - - +
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Residues in contact with VAL1030 (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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1015B GLU* 3.5 2.9 - - - -
1016B GLY 2.8 36.7 + - - +
1018B ALA* 3.5 29.2 - - + +
1028B THR* 4.2 4.7 - - + -
1029B ARG* 1.3 85.5 - - - +
1031B ALA* 1.3 60.6 + - - +
1032B ILE* 3.4 25.1 - - + -
1066B LEU* 3.3 33.2 - - + -
1078B ILE* 3.8 9.4 - - + -
1079B MET 3.3 9.4 - - - +
1080B GLU* 4.6 0.7 - - - -
1081B LEU* 3.7 12.4 - - - +
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Residues in contact with ALA1031 (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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2B 741 3.5 55.7 - - + +
1005B LEU* 4.4 1.3 - - + -
1013B VAL* 4.3 6.5 - - + -
1014B TYR 3.4 6.3 - - - +
1015B GLU* 4.6 0.2 - - - +
1030B VAL* 1.3 74.4 - - - +
1032B ILE* 1.3 61.4 + - - +
1077B VAL 3.5 0.9 - - - +
1078B ILE* 3.6 3.1 - - - -
1079B MET 2.9 35.0 + - - +
1081B LEU* 4.0 8.0 - - + +
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Residues in contact with ILE1032 (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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2B 741 4.1 1.1 - - - -
999B ILE* 3.8 20.0 - - + -
1000B THR 4.9 0.2 - - - +
1001B MET* 3.8 33.7 - - + -
1012B MET 3.5 1.6 - - - +
1013B VAL* 3.4 2.7 - - - -
1014B TYR* 2.6 51.4 + - + +
1016B GLY* 4.4 9.2 - - - +
1017B VAL 4.9 1.6 - - - +
1030B VAL* 3.4 33.4 - - + +
1031B ALA* 1.3 74.9 - - - +
1033B LYS* 1.3 62.2 + - - +
1076B LEU* 4.1 23.1 - - + -
1077B VAL 3.5 6.7 - - - +
1078B ILE* 3.8 16.4 - - + -
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Residues in contact with LYS1033 (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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2B 741 3.4 57.8 + - + +
1008B GLY* 3.5 5.5 - - - -
1009B SER* 2.7 37.5 + - - +
1010B PHE* 3.4 21.1 - - - +
1011B GLY* 3.6 20.0 - - - +
1012B MET 3.4 9.4 - - - +
1013B VAL* 4.5 4.8 - - + +
1032B ILE* 1.3 74.1 - - - +
1034B THR* 1.3 67.4 + - - +
1035B VAL* 4.9 1.1 - - + -
1047B PHE* 3.7 13.0 - - + -
1075B THR 3.3 1.3 - - - +
1076B LEU* 3.2 8.3 - - - +
1077B VAL* 3.0 34.5 + - + +
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Residues in contact with THR1034 (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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1001B MET* 3.9 24.7 - - + -
1011B GLY* 3.4 6.2 - - - -
1012B MET* 3.1 27.9 + - - +
1014B TYR* 3.5 20.3 + - + -
1033B LYS* 1.3 74.7 - - - +
1035B VAL* 1.3 63.2 + - - +
1036B ASN* 3.9 2.9 + - - -
1074B PRO* 4.2 15.9 - - + -
1075B THR 3.4 2.9 - - - -
1076B LEU* 3.1 30.5 - - + -
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Residues in contact with VAL1035 (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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1010B PHE* 3.5 27.6 - - + +
1033B LYS* 4.9 2.2 - - + +
1034B THR* 1.3 74.8 - - - +
1036B ASN* 1.3 61.9 + - - +
1039B ALA* 3.8 22.0 - - + -
1043B GLU* 6.0 1.1 - - + +
1044B ARG* 3.7 22.4 + - + +
1047B PHE* 3.3 46.2 - - + -
1074B PRO* 3.5 4.9 - - - +
1075B THR* 3.1 37.4 + - - +
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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