Contacts of the strand formed by residues 601 - 606 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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598A GLU* 2.9 47.5 + - + +
599A PRO 3.2 8.7 + - - +
600A GLY* 1.3 81.4 - - - +
602A MET* 1.3 63.8 + - - +
632A TRP* 3.5 35.4 - - + -
633A ILE 3.2 14.1 - - - +
634A GLU* 4.5 6.1 - - + -
635A PHE* 3.3 8.6 - - - -
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Residues in contact with MET 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532A VAL* 3.5 33.4 - - + -
534A LEU* 4.1 15.5 - - + -
559A VAL* 4.8 2.2 - - + -
594A CYS* 3.9 29.2 - - + -
596A ARG 3.5 11.9 - - - +
597A ILE* 4.1 5.8 - - + -
601A ARG* 1.3 76.1 - - - +
603A GLU* 1.3 60.8 + - - +
604A ILE* 3.9 13.7 - - + -
631A ARG 3.8 0.3 - - - +
632A TRP* 3.2 7.7 - - - -
633A ILE* 2.8 51.7 + - + +
635A PHE* 3.8 16.2 - - + -
638A LEU* 3.7 19.5 - - + -
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Residues in contact with GLU 603 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594A CYS* 3.3 7.1 - - - -
595A SER* 2.7 53.3 + - - +
596A ARG* 2.9 17.4 + - - +
602A MET* 1.3 72.8 - - - +
604A ILE* 1.3 61.3 + - - +
630A HIS* 3.8 28.2 + - + +
631A ARG* 3.3 13.0 - - - +
632A TRP* 3.5 30.7 + - + +
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Residues in contact with ILE 604 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559A VAL* 4.1 12.1 - - + -
589A LEU* 3.9 18.6 - - + -
592A HIS* 4.1 13.5 - - + -
593A PHE 3.1 14.1 - - - +
602A MET* 3.9 26.2 + - + -
603A GLU* 1.3 78.1 - - - +
605A TYR* 1.3 62.7 + - - +
629A SER 3.8 1.1 - - - +
630A HIS* 3.1 7.5 - - - +
631A ARG* 2.7 75.7 + - + +
633A ILE* 3.8 26.2 - - + -
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Residues in contact with TYR 605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499A LEU* 4.6 6.3 - - + +
500A THR* 4.7 10.4 - - - +
592A HIS* 2.9 32.0 - - - -
593A PHE* 2.9 50.8 + - + +
594A CYS 3.8 12.6 - - - -
595A SER* 3.9 12.6 - - - -
604A ILE* 1.3 77.4 - - - +
606A ASN* 1.3 75.3 + - - +
607A ILE* 4.3 18.8 - - + -
627A ASN* 3.8 11.7 - - - +
629A SER* 3.7 12.6 - - - +
630A HIS* 3.8 29.6 - + + +
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Residues in contact with ASN 606 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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591A ASP* 3.4 13.9 + - - +
592A HIS* 3.6 26.2 + - - +
605A TYR* 1.3 72.0 - - - +
607A ILE* 1.3 64.5 + - - +
608A TRP* 2.7 40.1 + - - +
609A GLY 3.0 8.6 + - - +
627A ASN* 3.0 21.7 + - - -
629A SER* 2.9 26.3 + - - +
582B HIS* 4.1 24.0 - - - +
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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