Contacts of the strand formed by residues 1064 - 1067 (chain N) in PDB entry 2FDB
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 HIS1064 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1055N GLN* 3.6 25.1 - - + +
1056N LEU 3.2 5.8 - - - +
1057N TYR* 3.8 16.9 + + + +
1063N LYS* 1.3 77.9 - - - +
1065N VAL* 1.3 64.8 + - - +
1066N GLN 3.5 0.3 + - - -
1075N ALA* 3.2 10.6 - - - -
1076N MET 3.4 0.2 + - - -
1077N ALA* 2.9 44.0 + - - +
1078N GLU* 3.8 0.4 - - - -
1079N ASP* 3.6 24.4 - - - -
1084N ALA* 4.0 18.2 - - + -
1177N ARG* 2.9 49.2 + - - -
3166R LEU* 3.7 13.4 - - + +
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Residues in contact with VAL1065 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1056N LEU* 2.8 39.8 + - + +
1058N SER* 5.4 0.4 - - - -
1064N HIS* 1.3 73.5 - - - +
1066N GLN* 1.3 64.3 + - - +
1073N ILE* 4.5 1.8 - - + -
1074N ASN 3.3 10.1 - - - +
1075N ALA* 4.0 3.1 - - + +
1084N ALA* 3.4 22.7 - - - +
1086N LEU* 4.2 11.1 - - + +
1108N ILE* 3.9 28.0 - - + -
1151N MET* 4.7 4.0 - - - -
1153N PHE* 3.3 37.5 - - + -
1174N PHE* 3.9 12.3 - - + -
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Residues in contact with GLN1066 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1065N VAL* 1.3 76.4 - - - +
1067N VAL* 1.3 65.6 + - - +
1068N LEU* 3.5 29.4 - - + +
1072N ARG 3.8 0.2 - - - +
1073N ILE* 3.4 8.1 - - - +
1074N ASN* 2.8 58.2 + - - +
1076N MET* 4.0 5.7 + - - +
1077N ALA* 3.7 31.9 - - + +
1081N ASP* 4.0 7.6 + - - +
1083N PHE* 3.2 29.1 - - + +
1086N LEU* 5.3 0.4 - - - -
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Residues in contact with VAL1067 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1066N GLN* 1.3 78.0 - - - +
1068N LEU* 1.3 61.6 + - - +
1072N ARG 3.6 2.9 - - - +
1073N ILE* 4.1 8.1 - - + -
1083N PHE* 3.2 19.1 + - - +
1086N LEU* 4.8 4.0 - - + -
1101N GLY* 4.5 18.9 - - - -
1103N GLU* 5.5 0.2 - - - +
1104N THR* 3.4 22.4 - - - +
1106N LEU* 3.8 23.8 - - + +
1108N ILE* 3.7 34.3 - - + -
1118N ALA* 3.7 29.8 - - + -
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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