Contacts of the strand formed by residues 620 - 628 (chain M) 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 620 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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612M THR* 3.9 22.5 - - - +
613M GLU 4.0 3.4 - - - +
614M LYS* 3.5 24.0 - - + -
618M GLY 3.1 3.8 + - - -
619M GLN* 1.3 70.5 - - - +
621M ILE* 1.3 62.1 + - - +
622M TRP 3.8 14.8 - - - +
623M GLU* 3.3 39.7 + - - +
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Residues in contact with ILE 621 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613M GLU* 2.8 41.8 + - + +
614M LYS 5.1 2.0 - - - -
615M THR* 3.8 23.1 - - + -
619M GLN* 3.5 18.8 - - + +
620M GLN* 1.3 74.8 - - - +
622M TRP* 1.3 61.5 + - + +
646M ARG* 3.7 33.8 + - - +
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Residues in contact with TRP 622 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611M PHE* 3.9 21.1 - - + -
612M THR* 3.0 16.6 - - - -
613M GLU* 2.9 47.2 + - + +
620M GLN* 3.5 6.3 + - - +
621M ILE* 1.3 82.4 - - - +
623M GLU* 1.3 69.1 + - - +
624M MET* 3.7 37.6 - - + +
643M PRO* 4.5 0.9 - - + -
644M GLU 3.7 18.4 - - - -
645M TYR* 3.8 14.6 - + - -
646M ARG* 3.5 45.5 - - + +
656M VAL* 3.7 23.8 - - + -
675M TYR* 3.7 27.8 - + - -
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Residues in contact with GLU 623 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610M VAL* 3.8 23.2 - - + +
611M PHE 3.3 3.8 - - - -
612M THR* 4.2 3.0 - - + +
620M GLN* 3.3 28.1 + - - +
622M TRP* 1.3 81.2 - - - +
624M MET* 1.3 72.6 + - - +
625M GLU 5.3 0.2 - - - +
659M TYR* 4.8 4.9 + - - -
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Residues in contact with MET 624 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610M VAL* 3.7 3.1 - - - -
611M PHE* 2.7 40.7 + - - +
622M TRP* 3.7 36.1 - - + +
623M GLU* 1.3 81.3 - - - +
625M GLU* 1.3 76.2 + - - +
626M ALA 3.7 0.2 + - - -
643M PRO* 3.8 21.3 - - + -
644M GLU 4.8 5.6 - - - +
646M ARG* 6.3 1.1 - - - -
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Residues in contact with GLU 625 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608M LYS* 3.7 31.8 + - - +
609M VAL 3.5 13.2 - - - +
610M VAL* 4.4 12.1 - - + +
623M GLU* 5.3 1.0 - - - +
624M MET* 1.3 90.2 - - - +
626M ALA* 1.3 72.3 + - - +
627M THR 4.2 0.3 + - - -
643M PRO* 4.6 2.1 - - - +
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Residues in contact with ALA 626 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609M VAL* 2.8 20.2 + - + +
611M PHE* 3.9 13.0 - - + -
624M MET 3.7 0.4 + - - -
625M GLU* 1.3 84.3 - - - +
627M THR* 1.3 64.4 + - - +
628M VAL* 3.7 10.6 + - - +
640M VAL* 3.3 23.1 - - + -
641M GLU 3.9 10.5 - - - +
643M PRO* 3.9 18.6 - - + -
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Residues in contact with THR 627 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625M GLU 4.2 0.4 + - - -
626M ALA* 1.3 72.2 - - - +
628M VAL* 1.3 70.2 + - - +
640M VAL* 2.9 5.2 - - - +
641M GLU* 2.7 60.0 + - + +
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Residues in contact with VAL 628 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605M SER 5.9 0.9 - - - +
607M SER* 4.5 14.6 - - - +
608M LYS* 4.7 1.6 - - - -
609M VAL* 4.0 28.3 - - + +
626M ALA 3.7 10.1 + - - +
627M THR* 1.3 88.7 - - - +
629M ASP* 1.3 62.6 + - - +
630M LYS* 2.9 26.4 + - + +
633M SER* 3.3 21.1 - - - +
638M LEU* 4.4 13.7 - - + -
639M PHE 3.1 12.3 - - - +
640M VAL* 4.3 2.0 - - + -
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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