Contacts of the strand formed by residues 595 - 601 (chain L) in PDB entry 2O93
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 GLN 595 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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584L ASP* 4.5 4.0 - - - +
585L THR* 4.2 8.0 + - - -
593L GLY 4.1 0.4 + - - -
594L GLN* 1.3 76.9 - - - +
596L MET* 1.3 66.7 + - - +
597L ILE* 4.0 13.6 + - - +
629L ASP* 4.5 5.8 + - + +
632L LYS* 4.0 16.2 - - - +
639L PHE* 3.3 36.6 - - + +
640L VAL 3.2 13.0 - - - +
641L GLU* 4.7 1.3 - - - +
642L ILE* 4.9 0.4 - - - -
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Residues in contact with MET 596 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583L GLN* 4.3 6.5 - - + +
584L ASP* 3.4 11.9 - - - +
585L THR* 4.0 25.8 - - - +
594L GLN 3.9 0.4 + - - -
595L GLN* 1.3 75.5 - - - +
597L ILE* 1.3 71.1 + - - +
598L LEU* 3.5 36.7 + - + -
609L VAL* 5.3 0.4 - - + -
611L PHE* 4.6 14.6 - - + -
638L LEU 3.5 3.1 - - - +
639L PHE* 3.5 0.9 - - - -
640L VAL* 2.6 59.6 + - + +
642L ILE* 4.0 17.5 - - + -
658L PHE* 4.2 16.4 - - + -
673L PHE* 4.8 9.6 - - - -
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Residues in contact with ILE 597 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583L GLN* 3.2 4.0 - - - -
584L ASP* 2.8 53.7 + - + +
595L GLN* 4.0 11.2 - - - +
596L MET* 1.3 74.4 - - - +
598L LEU* 1.3 71.6 + - - +
599L THR* 4.4 1.1 + - - +
637L MET* 3.7 17.3 - - + -
638L LEU 3.7 4.0 - - - +
639L PHE* 3.3 42.8 - - + -
616M THR* 3.6 28.4 - - + +
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Residues in contact with LEU 598 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580L VAL* 4.2 9.4 - - + -
582L ARG 3.2 4.7 - - - +
583L GLN* 3.4 28.5 - - + -
596L MET* 3.5 27.4 - - + -
597L ILE* 1.3 76.5 - - - +
599L THR* 1.3 66.1 + - - +
600L GLY 4.2 0.4 - - - -
603L PHE* 4.2 11.0 - - + -
609L VAL* 4.9 1.6 - - + -
636L ASN 3.6 0.2 - - - +
637L MET* 3.4 6.8 - - - -
638L LEU* 3.0 41.8 + - + +
640L VAL* 4.5 13.0 - - + -
658L PHE* 3.7 27.4 - - + -
660L VAL* 4.1 21.8 - - + -
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Residues in contact with THR 599 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580L VAL* 4.6 0.2 - - - -
581L GLU* 2.6 33.6 + - + +
582L ARG* 2.6 33.1 + - + +
583L GLN* 5.6 0.2 - - - -
597L ILE* 4.4 1.4 + - - +
598L LEU* 1.3 76.3 + - - +
600L GLY* 1.3 56.2 + - - +
603L PHE* 4.3 2.0 - - - -
636L ASN 3.3 8.3 - - - +
614M LYS* 4.8 12.3 - - + +
615M THR 3.5 21.3 - - - +
616M THR* 3.2 34.3 + - - +
618M GLY* 3.9 14.4 - - - -
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Residues in contact with GLY 600 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579L MET 2.8 15.3 - - - -
581L GLU* 3.8 13.9 - - - -
599L THR* 1.3 76.8 - - - +
601L GLN* 1.3 65.6 + - - +
603L PHE* 3.7 7.6 - - - -
636L ASN* 2.9 35.1 + - - +
614M LYS* 4.7 3.6 + - - -
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Residues in contact with GLN 601 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579L MET* 2.8 60.1 + - + +
581L GLU* 2.6 26.8 - - - +
600L GLY* 1.3 77.5 - - - +
602L ASN* 1.3 77.4 + - - +
603L PHE* 3.3 7.4 - - - -
635L PRO 3.8 3.1 - - - -
636L ASN* 4.6 1.8 - - + +
614M LYS* 5.1 4.5 - - - +
667M ARG* 3.9 23.3 + - - +
670M PRO* 4.7 2.3 - - - +
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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