Contacts of the strand formed by residues 1004 - 1009 (chain C) in PDB entry 3EI4
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 VAL1004 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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955C SER* 2.6 33.8 + - - -
956C ALA* 3.5 8.7 - - - +
968C ALA* 3.9 25.2 - - + +
969C GLU 5.9 0.2 + - - -
974C LEU* 4.6 1.3 - - + -
1000C LEU* 3.8 27.8 - - + -
1002C GLU 4.7 1.1 - - - +
1003C PHE* 1.3 74.0 - - - +
1005C ASN* 1.3 65.2 + - - +
1006C VAL 3.6 3.1 - - - +
1007C PHE* 3.9 17.0 - - + -
1030C PHE* 3.6 32.3 - - + -
1031C GLY 3.4 13.5 - - - +
1032C THR* 5.3 1.3 - - - +
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Residues in contact with ASN1005 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358C PRO* 4.7 4.0 + - - +
359C ILE 3.1 22.7 + - - +
360C VAL* 3.6 22.4 - - - +
955C SER* 4.2 4.1 + - - +
956C ALA* 4.3 2.5 - - - -
1003C PHE* 3.4 22.7 + - - -
1004C VAL* 1.3 74.6 - - - +
1006C VAL* 1.3 76.7 + - - +
1031C GLY 2.8 17.1 + - - +
1033C VAL* 4.9 6.7 - - - +
77D LYS* 3.1 52.6 + - - +
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Residues in contact with VAL1006 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359C ILE* 4.8 2.0 - - + -
360C VAL 3.5 17.7 - - - +
361C ASP* 3.1 29.2 - - - +
362C MET* 3.3 41.3 - - + +
723C LYS* 5.7 2.5 - - - -
915C LYS* 5.1 2.9 - - - +
956C ALA* 3.6 13.7 - - - +
1004C VAL* 3.6 1.5 - - - +
1005C ASN* 1.3 84.8 - - + +
1007C PHE* 1.3 66.7 + - - +
1030C PHE* 3.4 4.9 - - - +
1031C GLY* 3.1 18.5 + - - +
77D LYS* 4.6 5.8 - - - +
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Residues in contact with PHE1007 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362C MET* 5.9 0.2 - - - -
915C LYS* 2.8 22.2 + - - +
956C ALA* 3.6 25.1 - - + +
957C VAL* 3.6 23.6 - - - +
958C GLU* 3.5 26.0 - - + +
966C LEU* 3.6 33.2 - - + -
968C ALA* 4.0 19.3 - - + -
974C LEU* 4.2 7.6 - - + -
1004C VAL* 3.9 16.2 - - + -
1006C VAL* 1.3 78.7 - - - +
1008C CYS* 1.3 67.1 + - - +
1028C VAL* 3.9 10.3 - - + -
1029C LEU 3.4 2.5 - - - -
1030C PHE* 3.4 37.2 - + + -
1040C VAL* 5.0 0.2 - - + -
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Residues in contact with CYS1008 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362C MET* 4.1 35.7 - - - +
363C CYS* 4.4 0.4 - - - -
364C VAL* 3.8 23.1 - - - -
915C LYS* 4.9 2.0 - - - +
958C GLU* 3.6 8.1 - - - -
1006C VAL* 5.9 0.2 - - + -
1007C PHE* 1.3 78.8 - - - +
1009C HIS* 1.3 72.2 + - - +
1028C VAL* 3.9 5.6 - - - +
1029C LEU* 2.8 39.0 + - - +
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Residues in contact with HIS1009 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364C VAL* 3.4 19.4 - - - +
915C LYS* 5.8 0.7 - - + -
958C GLU* 3.0 37.2 + - - -
959C ILE* 3.1 18.9 + - + -
960C LEU* 4.9 4.8 + - - -
1008C CYS* 1.3 82.8 - - - +
1010C GLY* 1.3 60.9 + - - +
1027C SER 3.4 12.6 - - - +
1028C VAL* 4.0 17.9 - - + +
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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