Contacts of the strand formed by residues 1012 - 1018 (chain J) 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 MET1012 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1094B LEU* 4.7 14.4 - - + +
1105B ALA* 3.7 14.3 - - + +
1106B PRO* 3.2 41.1 - - + +
1107B PRO* 3.7 5.8 - - + -
1208B LEU* 5.0 0.7 - - + -
1004J GLU* 3.4 26.5 - - + +
1006J GLY* 3.6 19.3 - - - +
1007J GLN* 4.0 17.9 - - - +
1008J GLY 4.3 0.4 - - - +
1011J GLY* 1.3 73.2 - - - -
1013J VAL* 1.3 66.6 + - - +
1014J TYR* 3.4 26.9 - - + -
1032J ILE 3.8 0.5 - - - +
1033J LYS* 3.3 1.7 - - - -
1034J THR* 2.9 36.5 + - - +
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Residues in contact with VAL1013 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10J 741 3.8 48.2 - - + +
1004J GLU* 3.7 3.6 - - - -
1005J LEU* 2.8 35.5 + - + -
1006J GLY 3.0 14.8 + - - +
1007J GLN 4.8 0.7 - - - -
1008J GLY* 4.0 22.9 - - - +
1012J MET* 1.3 78.6 - - - +
1014J TYR* 1.3 74.9 + - - +
1031J ALA* 4.2 5.8 - - + -
1032J ILE 3.4 5.8 - - - +
1033J LYS* 4.1 15.5 - - + -
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Residues in contact with TYR1014 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1107B PRO* 3.5 6.4 - - - +
1108B SER* 2.9 37.5 + - - -
1111B LYS* 3.6 27.9 - - + +
1001J MET* 3.7 35.2 - - + -
1003J ARG* 3.8 7.2 - - - -
1004J GLU* 3.4 47.1 + - + -
1005J LEU* 3.7 9.3 - - - +
1012J MET* 3.4 28.8 - - + +
1013J VAL* 1.3 77.6 - - - +
1015J GLU* 1.3 60.6 + - - +
1031J ALA* 3.4 6.1 - - - -
1032J ILE* 2.6 36.9 + - + +
1034J THR* 4.2 6.3 - - + -
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Residues in contact with GLU1015 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1001J MET* 3.8 2.1 - - - -
1002J SER* 2.8 37.4 + - - +
1003J ARG* 3.0 47.6 + - - +
1005J LEU* 3.7 18.7 - - + +
1014J TYR* 1.3 75.7 - - - +
1016J GLY* 1.3 64.5 + - - +
1029J ARG* 2.5 40.6 + - + -
1030J VAL 3.7 3.6 - - - +
1032J ILE* 4.8 0.4 - - - -
1081J LEU* 3.6 19.9 - - + +
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Residues in contact with GLY1016 (chain J).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1000J THR 3.1 13.9 - - - -
1001J MET* 4.3 0.2 - - - -
1002J SER* 4.3 4.9 - - - -
1014J TYR 4.1 0.2 + - - -
1015J GLU* 1.3 79.7 - - - +
1017J VAL* 1.3 62.4 + - - +
1029J ARG* 3.5 6.6 - - - +
1030J VAL* 2.8 39.9 + - - -
1032J ILE* 3.9 9.3 - - - +
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Residues in contact with VAL1017 (chain J).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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998J LYS 3.7 0.5 - - - +
999J ILE* 3.6 2.6 - - - +
1000J THR* 2.9 48.7 + - + +
1016J GLY* 1.3 75.9 - - - +
1018J ALA* 1.3 65.8 + - - +
1019J LYS* 4.5 2.9 - - + +
1027J GLU* 3.9 41.7 - - + +
1028J THR 3.4 10.8 - - - +
1029J ARG* 4.9 9.9 - - + -
1030J VAL* 4.2 2.2 - - - -
1032J ILE* 5.3 0.2 - - - -
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Residues in contact with ALA1018 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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998J LYS 3.4 4.0 - - - -
999J ILE* 3.4 20.9 - - + -
1017J VAL* 1.3 75.1 - - - +
1019J LYS* 1.3 65.4 + - - +
1020J GLY 3.5 2.4 + - - -
1021J VAL* 3.4 30.1 - - + +
1027J GLU* 3.7 0.2 - - - -
1028J THR 2.9 28.0 + - - -
1030J VAL* 3.8 21.3 - - + +
1078J ILE* 4.4 2.7 - - + -
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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