Contacts of the strand formed by residues 1072 - 1078 (chain B) in PDB entry 6ZGI
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 GLU1072 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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713B ALA* 3.9 13.8 - - + +
714B ILE 3.3 10.5 - - - +
715B PRO* 4.0 2.7 - - + -
716B THR* 5.0 0.2 - - - -
1070B ALA 4.1 3.1 + - - +
1071B GLN* 1.3 74.7 - - - +
1073B LYS* 1.3 61.2 + - - +
1321B NAG 3.2 35.6 - - + +
892C ALA* 4.6 12.7 - - - +
893C ALA 3.9 9.3 - - - +
894C LEU* 3.1 35.1 - - + +
895C GLN* 5.1 1.6 - - - +
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Residues in contact with LYS1073 (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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713B ALA* 3.2 5.6 - - - -
714B ILE 2.9 31.5 + - - +
716B THR* 4.4 12.8 - - + -
1072B GLU* 1.3 75.3 - - - +
1074B ASN* 1.3 67.8 + - - +
1075B PHE* 3.4 42.6 - - + -
1098B ASN* 6.3 0.6 - - - +
1110B TYR* 4.8 10.6 + - - -
1321B NAG 4.4 4.9 - - + -
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Residues in contact with ASN1074 (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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711B SER* 4.9 5.2 - - - +
712B ILE 3.5 3.4 - - - +
713B ALA* 4.1 6.2 - - - +
1073B LYS* 1.3 80.8 - - - +
1075B PHE* 1.3 71.6 + - - +
1321B NAG 1.4 65.7 + - - +
895C GLN* 3.0 24.1 + - - +
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Residues in contact with PHE1075 (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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711B SER* 3.4 6.4 + - - -
712B ILE* 2.9 38.5 + - + +
714B ILE* 3.6 32.8 - - + -
716B THR* 5.7 0.2 - - + -
1073B LYS* 3.4 59.5 - - + -
1074B ASN* 1.3 75.2 - - - +
1076B THR* 1.3 61.3 + - - +
1096B VAL* 3.9 23.6 - - + -
1097B SER 3.8 21.8 - - - +
1098B ASN* 4.7 8.3 - - + -
1110B TYR* 3.6 39.9 - + - -
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Residues in contact with THR1076 (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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710B ASN* 3.6 24.7 - - - +
711B SER* 5.6 0.9 - - - -
1075B PHE* 1.3 73.9 - - - +
1077B THR* 1.3 61.8 + - - +
1096B VAL* 3.4 4.2 - - - +
1097B SER* 2.9 53.2 + - - -
1099B GLY* 4.9 4.0 + - - -
1102B TRP* 4.0 6.2 - - - -
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Residues in contact with THR1077 (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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710B ASN* 3.8 18.8 + - - +
711B SER 3.9 18.6 - - - +
712B ILE* 4.1 18.8 - - + -
1076B THR* 1.3 75.9 - - - +
1078B ALA* 1.3 67.6 + - - +
1094B VAL* 3.9 2.6 - - - +
1095B PHE 2.7 21.5 + - - -
1102B TRP* 3.9 7.0 - - - -
1133B VAL* 5.5 0.3 - - - +
897C PRO* 4.0 11.9 - - + -
900C MET* 3.5 36.6 - - - +
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Residues in contact with ALA1078 (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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1077B THR* 1.3 84.0 + - - +
1079B PRO* 1.3 74.8 - - + +
1080B ALA 4.0 6.3 - - - +
1081B ILE* 5.2 0.4 - - + -
1090B PRO* 6.0 0.2 - - - +
1095B PHE* 3.7 21.2 + - + +
1102B TRP* 3.7 21.5 - - + -
1131B GLY 4.2 0.9 - - - +
1133B VAL* 3.7 30.1 - - + -
900C MET* 4.3 8.2 - - - +
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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