Contacts of the strand formed by residues 601 - 606 (chain B) in PDB entry 1O94
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 ARG 601 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598B GLU* 2.9 54.0 + - + +
599B PRO 3.3 16.7 + - - +
600B GLY* 1.3 80.4 + - - +
602B MET* 1.3 64.6 + - - +
632B TRP* 3.8 20.2 - - + -
633B ILE 3.3 13.2 - - - +
634B GLU* 4.6 7.6 - - + +
635B PHE* 3.4 7.4 - - - -
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Residues in contact with MET 602 (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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532B VAL* 3.6 29.4 - - + -
534B LEU* 4.2 14.1 - - + -
559B VAL* 4.9 1.8 - - + -
594B CYS* 3.9 29.8 - - + -
596B ARG 3.5 11.7 - - - +
597B ILE* 4.2 6.1 - - + -
601B ARG* 1.3 78.8 - - - +
603B GLU* 1.3 60.1 + - - +
604B ILE* 3.8 12.1 + - + -
631B ARG 3.8 0.5 - - - +
632B TRP* 3.4 7.8 - - - -
633B ILE* 2.9 46.3 + - + +
635B PHE* 3.8 14.8 - - + -
638B LEU* 3.8 24.7 - - + -
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Residues in contact with GLU 603 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594B CYS* 3.2 8.1 - - - -
595B SER* 2.7 51.1 + - - +
596B ARG* 2.9 51.5 + - + +
602B MET* 1.3 73.8 - - - +
604B ILE* 1.3 62.8 + - - +
630B HIS* 3.8 30.8 - - + +
631B ARG 3.4 11.4 - - - +
632B TRP* 3.6 28.5 + - + -
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Residues in contact with ILE 604 (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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559B VAL* 4.2 12.3 - - + -
589B LEU* 3.8 29.4 - - + -
592B HIS* 4.1 10.5 - - + -
593B PHE 3.1 13.9 - - - +
594B CYS* 4.3 1.1 - - + +
602B MET* 4.1 26.2 - - + -
603B GLU* 1.3 79.8 - - - +
605B TYR* 1.3 62.2 + - - +
629B SER 3.9 1.1 - - - +
630B HIS* 3.1 6.9 - - - +
631B ARG* 2.9 61.9 + - + +
633B ILE* 4.0 30.1 - - + -
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Residues in contact with TYR 605 (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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499B LEU* 4.6 5.1 - - + +
500B THR* 4.6 10.7 - - - +
592B HIS* 3.1 10.9 - - - -
593B PHE* 3.0 67.8 + - + +
594B CYS 3.9 2.6 + - - -
595B SER* 3.8 33.4 - - - -
604B ILE* 1.3 75.9 - - - +
606B ASN* 1.3 70.6 + - - +
607B ILE* 4.3 19.1 - - + -
627B ASN* 3.8 9.6 - - - +
629B SER* 3.7 13.2 - - - +
630B HIS* 3.8 25.1 - + + +
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Residues in contact with ASN 606 (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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582A HIS* 3.8 25.3 - - - +
591B ASP* 3.4 13.4 + - - +
592B HIS* 3.6 27.1 + - - +
605B TYR* 1.3 70.5 - - - +
607B ILE* 1.3 61.6 + - - +
608B TRP* 2.8 40.9 + - - +
609B GLY 3.2 2.2 + - - +
627B ASN* 2.9 25.8 + - - -
629B SER* 2.9 24.2 + - - +
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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