Contacts of the strand formed by residues 1012 - 1018 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1004K GLU* 4.1 25.6 - - + +
1006K GLY* 3.8 20.6 - - - +
1007K GLN* 4.2 25.9 - - - +
1008K GLY 4.2 1.3 - - - +
1011K GLY* 1.3 73.3 - - - -
1013K VAL* 1.3 68.7 + - - +
1014K TYR* 3.5 30.8 - - + +
1032K ILE 3.9 0.5 - - - +
1033K LYS* 3.2 4.5 - - - -
1034K THR* 3.1 33.7 + - - +
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Residues in contact with VAL1013 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K 741 3.7 52.0 - - + +
1004K GLU* 3.5 6.2 - - - +
1005K LEU* 2.6 34.8 + - + -
1006K GLY 2.8 22.5 + - - +
1007K GLN 4.5 1.3 - - - +
1008K GLY* 3.9 21.5 - - - -
1011K GLY 4.4 0.2 - - - +
1012K MET* 1.3 79.4 - - - +
1014K TYR* 1.3 65.8 + - - +
1031K ALA* 4.2 5.8 - - + -
1032K ILE 3.5 11.4 - - - +
1033K LYS* 4.5 8.7 - - + -
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Residues in contact with TYR1014 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1001K MET* 3.6 37.9 - - + -
1002K SER 4.2 8.5 - - - -
1003K ARG 3.6 6.1 - - - +
1004K GLU* 3.1 50.8 + - + +
1005K LEU* 3.4 13.4 - - - +
1012K MET* 3.5 31.6 - - + +
1013K VAL* 1.3 78.3 - - - +
1015K GLU* 1.3 66.2 + - - +
1031K ALA* 3.4 0.9 - - - -
1032K ILE* 2.7 41.9 + - + +
1034K THR* 4.1 14.1 - - + -
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Residues in contact with GLU1015 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K 741 6.0 0.2 - - - +
1001K MET* 3.6 3.7 - - - -
1002K SER* 2.8 36.4 + - - +
1003K ARG* 2.9 49.3 + - - +
1005K LEU* 3.6 18.3 - - + +
1014K TYR* 1.3 75.6 - - - +
1016K GLY* 1.3 65.7 + - - +
1029K ARG* 2.7 36.4 + - - +
1030K VAL 3.6 9.4 - - - +
1032K ILE* 5.0 0.9 - - - -
1081K LEU* 4.2 12.4 - - + +
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Residues in contact with GLY1016 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1000K THR 3.0 13.2 - - - -
1001K MET* 4.1 2.0 - - - -
1002K SER* 4.2 4.3 - - - -
1014K TYR 4.1 0.2 + - - -
1015K GLU* 1.3 81.4 - - - +
1017K VAL* 1.3 64.5 + - - +
1029K ARG* 3.6 6.2 - - - +
1030K VAL* 2.8 41.6 + - - +
1032K ILE* 4.4 3.8 - - - +
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Residues in contact with VAL1017 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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998K LYS 3.6 1.4 - - - +
999K ILE* 3.6 2.6 - - - +
1000K THR* 2.8 49.3 + - + +
1016K GLY* 1.3 76.6 - - - +
1018K ALA* 1.3 64.8 + - - +
1019K LYS* 4.6 3.1 - - + +
1027K GLU* 3.8 39.9 - - + +
1028K THR 3.3 8.3 - - - +
1029K ARG* 4.8 12.6 - - + -
1030K VAL* 4.3 2.0 - - - -
1032K ILE* 4.9 0.2 - - - +
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Residues in contact with ALA1018 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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998K LYS 3.3 4.5 - - - -
999K ILE* 3.6 21.1 - - + -
1017K VAL* 1.3 74.0 - - - +
1019K LYS* 1.3 64.0 + - - +
1020K GLY 3.3 3.5 + - - -
1021K VAL* 3.5 30.0 - - + +
1027K GLU 3.9 0.2 - - - -
1028K THR* 2.9 26.2 + - - -
1030K VAL* 3.6 21.3 - - + +
1078K ILE* 4.4 2.9 - - + -
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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