Contacts of the strand formed by residues 1004 - 1009 (chain B) in PDB entry 4EC0
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 TYR1004 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1002B PRO* 3.5 39.5 + - + +
1003B ASN* 1.3 81.0 + - - +
1005B LYS* 1.3 59.7 + - - +
1006B LEU 4.1 0.4 - - - -
1022B PHE* 3.7 12.8 - + + -
1027B ILE* 3.5 36.8 - - + +
1028B GLN 3.9 5.5 + - - +
1029B TYR* 3.4 17.3 - - + +
1030B GLU* 2.9 25.7 + - - +
1054B LEU* 3.7 17.7 - - + -
1055B GLU 3.5 0.7 - - - -
1056B VAL* 3.8 31.2 - - + -
1070B TYR* 4.4 8.1 + + - -
1071B LEU* 3.7 25.6 - - + +
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Residues in contact with LYS1005 (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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1003B ASN* 4.1 9.2 + - - +
1004B TYR* 1.3 72.7 - - - +
1006B LEU* 1.3 60.2 + - - +
1007B THR* 3.8 11.7 + - - +
1030B GLU* 3.6 35.0 + - + +
1032B HIS* 3.7 38.3 + - + -
1053B ILE 4.0 0.2 - - - +
1054B LEU* 3.4 4.3 - - - +
1055B GLU* 2.9 66.9 + - + +
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Residues in contact with LEU1006 (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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1004B TYR 4.1 0.6 - - - -
1005B LYS* 1.3 71.2 - - - +
1007B THR* 1.3 62.4 + - - +
1008B TYR* 5.1 1.1 - - + +
1015B ALA* 4.1 11.2 - - + -
1018B ILE* 4.0 38.4 - - + -
1019B ARG* 3.7 38.8 - - + +
1022B PHE* 4.8 0.2 - - + -
1029B TYR* 4.1 11.9 - - + -
1030B GLU 2.8 14.8 + - - +
1031B ASP* 3.9 6.5 - - - +
1032B HIS* 2.8 33.7 + - - +
1052B PRO* 4.1 12.6 - - + -
1053B ILE 3.4 17.9 - - - +
1054B LEU* 3.8 13.1 - - + +
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Residues in contact with THR1007 (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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1005B LYS* 3.8 14.8 + - - +
1006B LEU* 1.3 74.4 - - - +
1008B TYR* 1.3 63.8 + - - +
1032B HIS* 3.1 30.7 + - + +
1034B ILE* 3.8 18.2 - - + -
1042B ILE* 4.6 14.4 - - + -
1051B ILE* 3.7 13.8 - - + +
1052B PRO* 3.2 26.3 - - - +
1053B ILE* 3.0 32.1 + - + +
1055B GLU* 4.6 1.7 + - - -
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Residues in contact with TYR1008 (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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1006B LEU* 4.1 2.0 - - + -
1007B THR* 1.3 75.4 - - - +
1009B PHE* 1.3 85.2 + + - +
1011B MET* 3.7 29.2 - - + -
1012B ARG 3.6 17.7 - - - -
1013B GLY* 3.6 4.5 - - - -
1014B ARG* 2.9 22.8 + - + +
1015B ALA* 3.3 26.9 - - + -
1019B ARG* 4.0 5.2 - - - +
1032B HIS 3.1 5.6 + - - -
1033B ARG* 3.2 7.8 - - - -
1034B ILE* 3.0 29.8 + - - +
1051B ILE* 3.9 18.6 - - + -
1052B PRO* 3.5 36.6 - - + -
1201B GSH 3.3 28.9 - - + -
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Residues in contact with PHE1009 (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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1008B TYR* 1.3 104.1 - + + +
1010B ASN* 1.3 61.0 + - - +
1011B MET* 2.9 31.1 + - + +
1019B ARG* 3.7 6.6 + - - -
1033B ARG* 4.3 1.3 - - - +
1034B ILE* 3.7 34.5 - - + -
1036B GLN* 2.9 33.7 - - - -
1039B TRP* 4.0 21.1 - + - -
1051B ILE* 3.6 20.2 - - + +
1201B GSH 4.1 26.0 - - + -
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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