Contacts of the strand formed by residues 578 - 583 (chain B) in PDB entry 1OH7
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 ILE 578 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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577B GLY* 1.3 79.0 - - - +
579B ARG* 1.3 62.6 + - - +
580B ILE* 3.4 33.4 - - + -
601B LEU* 3.4 11.8 - - + +
603B LEU* 2.8 40.5 + - + +
627B THR* 3.9 13.9 - - + +
630B ILE* 5.8 1.3 - - + -
631B ALA* 5.3 1.3 - - + +
645B VAL* 5.3 2.2 - - + -
646B GLU 3.5 4.9 - - - +
647B ILE* 4.3 24.9 - - + +
650B ILE* 4.8 6.1 - - + -
689B LEU* 3.3 37.7 - - + -
722B LEU* 4.0 14.0 - - + +
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Residues in contact with ARG 579 (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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573B ILE* 3.7 28.1 - - - +
577B GLY 6.0 1.0 - - - -
578B ILE* 1.3 76.2 - - - +
580B ILE* 1.3 61.2 + - - +
581B THR* 5.3 0.8 + - - -
601B LEU 3.1 5.2 - - - +
602B ASN* 3.4 27.3 + - + +
603B LEU 4.7 4.7 + - - +
604B SER* 5.6 8.7 - - - -
644B LYS* 3.7 2.5 - - + +
645B VAL* 3.2 6.2 - - - -
646B GLU* 2.9 79.3 + - + +
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Residues in contact with ILE 580 (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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578B ILE* 3.4 26.5 - - + -
579B ARG* 1.3 76.2 - - - +
581B THR* 1.3 64.7 + - - +
583B GLY* 3.4 34.8 - - - +
599B ASN 3.9 6.5 - - - +
600B PRO* 3.2 6.4 - - - +
601B LEU* 2.9 51.8 + - + +
626B GLN* 5.4 3.4 - - + +
627B THR* 4.7 8.1 - - + +
630B ILE* 4.1 24.2 - - + -
642B ALA* 4.2 4.0 - - + -
644B LYS 3.4 5.8 - - - +
645B VAL* 3.8 17.0 - - + -
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Residues in contact with THR 581 (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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579B ARG 5.3 1.0 + - - -
580B ILE* 1.3 72.0 + - - +
582B GLU* 1.3 79.0 + - + +
583B GLY 3.3 2.3 + - - -
600B PRO* 4.6 4.0 - - + -
642B ALA* 3.7 2.1 - - - +
643B GLN* 3.0 27.1 + - + -
644B LYS* 3.0 34.3 + - - +
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Residues in contact with GLU 582 (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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580B ILE 4.1 0.2 + - - -
581B THR* 1.3 82.6 - - + +
583B GLY* 1.3 62.3 + - - +
584B ARG* 3.6 10.9 + - - -
598B ALA* 3.5 33.0 - - + +
599B ASN* 3.7 13.3 + - - -
600B PRO* 4.4 4.9 - - - +
642B ALA* 3.4 11.8 - - - -
643B GLN* 3.7 24.5 + - + +
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Residues in contact with GLY 583 (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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580B ILE* 3.4 21.7 - - - +
581B THR 3.3 1.4 + - - -
582B GLU* 1.3 77.1 - - - +
584B ARG* 1.3 61.2 + - - -
596B PHE* 4.6 0.2 - - - -
598B ALA* 3.3 7.3 - - - -
599B ASN 3.1 22.6 + - - -
626B GLN* 3.0 17.2 + - - -
630B ILE* 4.3 2.2 - - - -
641B PRO 3.3 8.7 - - - -
642B ALA* 3.8 2.9 - - - -
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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