Contacts of the strand formed by residues 674 - 680 (chain B) in PDB entry 1M7X
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 LYS 674 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257A THR* 4.0 12.3 + - - +
590A GLU* 5.4 2.2 - - - +
673B GLY* 1.3 72.0 - - - -
675B TRP* 1.3 60.0 + - - +
696B THR* 3.8 25.4 - - + -
697B VAL 3.9 4.3 - - - -
698B HIS* 3.7 21.9 - - + +
725B ARG* 3.3 6.1 - - - +
726B GLU* 2.8 61.9 + - + +
727B ALA 4.3 7.9 + - - -
728B GLU* 2.6 37.6 + - - -
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Residues in contact with TRP 675 (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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650B GLU* 3.4 34.5 - - - -
652B ILE* 3.4 40.4 - - + -
669B ILE* 4.1 6.8 - - + +
671B GLN* 3.2 41.5 + - + -
673B GLY 3.2 20.9 + - - -
674B LYS* 1.3 76.5 - - - +
676B ARG* 1.3 61.0 + - - +
696B THR* 3.2 3.6 - - - -
697B VAL* 2.8 40.4 + - + +
711B LEU* 4.1 23.6 - - + -
723B LEU* 3.7 24.0 - - + +
724B VAL 3.1 17.0 - - - -
725B ARG* 3.7 28.4 - - + +
726B GLU* 5.5 0.4 - - - -
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Residues in contact with ARG 676 (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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589A LEU* 3.1 29.4 + - - +
590A GLU* 3.9 11.1 + - - +
597A HIS* 4.2 11.3 + - - -
675B TRP* 1.3 76.7 - - - +
677B GLU* 1.3 75.0 + - - +
678B ILE* 5.7 1.6 - - - -
694B GLY 5.3 0.8 + - - +
695B GLY* 4.0 17.6 - - - -
696B THR* 3.2 31.4 + - - +
723B LEU* 3.0 7.2 - - - -
724B VAL* 2.6 46.3 + - + +
726B GLU* 2.8 32.6 + - + +
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Residues in contact with GLU 677 (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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676B ARG* 1.3 87.9 - - - +
678B ILE* 1.3 61.6 + - - +
679B LEU 4.4 6.1 - - - +
680B ASN* 3.2 30.1 - - - +
692B GLY* 3.8 4.5 - - - -
693B ASN* 2.8 53.3 + - + +
696B THR 5.7 0.2 - - - +
721B ILE* 3.9 10.4 - - + +
722B TRP 3.2 8.5 - - - +
723B LEU* 3.7 22.6 - - + +
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Residues in contact with ILE 678 (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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278A TRP* 5.8 2.6 - - - -
609B THR* 3.9 24.2 + - + +
613B HIS* 3.8 34.5 - - + +
616B MET* 6.0 0.7 - - - -
651B ILE* 4.5 11.9 - - + -
676B ARG* 5.7 2.2 - - + -
677B GLU* 1.3 76.6 - - - +
679B LEU* 1.3 63.5 + - - +
722B TRP* 2.8 34.2 + - + +
723B LEU 4.5 0.2 - - - +
724B VAL* 3.3 40.4 - - + -
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Residues in contact with LEU 679 (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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555B GLY* 4.8 0.2 - - - -
602B LEU* 4.3 11.9 - - + -
605B ASP* 4.3 20.2 - - + +
606B LEU* 3.2 33.0 - - + +
609B THR* 4.5 4.9 - - + +
677B GLU* 3.5 3.4 - - - +
678B ILE* 1.3 82.1 + - - +
680B ASN* 1.3 65.1 + - - +
681B THR* 4.3 15.5 - - + -
686B TYR* 4.8 3.4 - - - +
720B THR* 4.3 5.4 - - - +
721B ILE* 3.0 5.9 - - - +
722B TRP* 2.7 81.6 + - + +
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Residues in contact with ASN 680 (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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677B GLU* 3.2 27.2 - - + +
679B LEU* 1.3 77.2 - - - +
681B THR* 1.3 64.7 + - - +
682B ASP* 2.9 26.6 + - - +
683B SER* 3.2 21.3 + - - +
686B TYR* 3.3 16.9 + - - -
691B ALA 3.0 20.5 - - - +
692B GLY* 4.1 1.2 - - - -
716B PRO* 3.9 3.8 - - - +
719B ALA* 4.7 0.8 - - - +
720B THR 3.7 4.0 + - - -
721B ILE* 3.3 19.8 - - + +
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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