Contacts of the strand formed by residues 1080 - 1085 (chain B) in PDB entry 3HOX
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 LYS1080 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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659A HIS 4.2 6.9 - - - +
1071B VAL* 4.8 5.6 - - + -
1072B MET 3.9 2.0 - - - +
1073B TYR* 3.2 35.9 - - + -
1074B ASN* 4.9 1.7 + - - +
1079B LYS* 1.3 95.7 - - - +
1081B LEU* 1.3 62.3 + - - +
1082B MET 3.7 2.5 + - - -
180C TYR* 3.0 43.9 + - - +
181C ASP* 3.4 27.1 + - - -
182C PRO* 5.3 1.4 - - - +
184C ASN* 4.3 15.2 - - - +
188C HIS* 3.6 25.7 - - + +
189C THR* 3.7 20.8 + - - +
191C TYR* 5.1 4.8 + - - -
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Residues in contact with LEU1081 (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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658A LEU 3.9 7.0 - - - +
659A HIS* 2.9 32.3 - - - +
660A ASN 3.5 1.1 - - - -
661A GLY* 3.3 29.8 - - - +
828B ALA* 6.3 1.1 - - + -
829B CYS 6.1 0.2 - - - +
830B TYR* 5.0 7.9 - - + -
1000B PRO* 4.5 15.9 - - + -
1071B VAL* 4.4 1.0 - - - +
1072B MET* 2.7 28.6 + - + +
1073B TYR 4.6 2.7 - - - -
1074B ASN* 4.3 12.8 - - + +
1080B LYS* 1.3 75.5 - - - +
1082B MET* 1.3 53.5 + - - +
1083B ALA* 2.4 38.1 + - + +
1085B ILE* 4.1 21.5 - - + -
188C HIS 4.0 1.3 - - - -
189C THR* 3.7 9.7 + - - -
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Residues in contact with MET1082 (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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659A HIS 4.1 3.2 + - - +
660A ASN* 3.0 37.7 + - - +
1079B LYS* 6.3 1.8 - - - +
1080B LYS 3.7 2.4 + - - -
1081B LEU* 1.3 67.9 - - - +
1083B ALA* 1.3 57.1 + - - +
187C LYS 3.1 21.3 - - - +
188C HIS* 3.3 14.6 + - - +
189C THR* 3.1 33.3 - - - +
190C ASP* 3.1 38.4 + - + +
22H LYS* 4.7 11.9 - - - +
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Residues in contact with ALA1083 (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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533A LYS* 5.8 3.8 - - - +
660A ASN* 3.4 14.4 + - - +
661A GLY* 3.9 17.9 - - - +
662A PHE* 4.3 8.7 - - + +
663A SER 5.2 0.4 - - - +
1071B VAL* 4.5 0.9 - - - +
1072B MET 4.5 3.6 + - - -
1081B LEU* 2.4 33.5 + - + +
1082B MET* 1.3 75.7 - - - +
1084B GLN* 1.3 81.2 + - - +
1085B ILE* 4.5 4.1 - - + +
189C THR* 4.4 0.7 - - - +
190C ASP 5.2 0.2 - - - -
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Residues in contact with GLN1084 (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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663A SER* 3.7 13.0 - - - -
742A ASN* 5.9 0.3 + - - -
1069B PHE* 4.0 17.8 - - + -
1070B GLU 3.0 14.8 - - - +
1071B VAL* 3.4 17.7 - - + -
1083B ALA* 1.3 90.0 - - - +
1085B ILE* 1.3 63.9 + - - +
189C THR* 2.7 27.2 - - - +
190C ASP 2.9 19.4 + - - +
191C TYR* 3.2 6.8 - - - +
192C TRP* 4.1 19.4 - - - +
201C TRP* 3.4 28.0 - - + -
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Residues in contact with ILE1085 (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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661A GLY* 6.4 0.7 - - - -
662A PHE 4.9 2.5 - - - +
663A SER* 3.7 4.5 - - - -
826B ALA* 4.1 4.0 - - + -
827B ILE 3.2 35.4 - - - +
828B ALA* 3.5 22.9 - - + -
1000B PRO* 5.8 1.1 - - + -
1069B PHE* 3.0 23.7 - - - -
1070B GLU 3.2 8.8 + - - +
1072B MET* 3.0 56.5 - - + +
1081B LEU* 4.1 18.6 - - + -
1083B ALA* 4.5 4.7 - - + +
1084B GLN* 1.3 81.4 - - - +
1086B PHE* 1.3 71.1 + - - +
1087B PHE 3.0 5.8 + - - -
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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