Contacts of the strand formed by residues 650 - 656 (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 GLU 650 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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629B LEU* 5.7 0.9 - - - +
642B VAL* 3.3 22.8 - - + +
643B ARG 3.0 4.7 - - - -
644B ARG* 3.2 44.0 + - + -
649B ASN* 1.3 73.4 - - - +
651B ILE* 1.3 63.5 + - - +
652B ILE* 5.2 1.4 - - - +
669B ILE* 5.6 0.5 - - - +
670B ASN* 3.4 33.5 + - - +
671B GLN* 3.3 36.2 + - - +
675B TRP* 3.4 25.6 - - + -
724B VAL* 5.3 1.0 - - - +
725B ARG* 4.7 5.7 + - - +
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Residues in contact with ILE 651 (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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613B HIS* 4.8 10.8 - - + +
615B ALA* 3.8 20.0 - - + -
616B MET* 3.2 27.4 - - - -
642B VAL* 3.3 4.6 - - - +
643B ARG* 3.0 26.1 + - + -
649B ASN* 5.6 1.6 - - + -
650B GLU* 1.3 79.0 - - - +
652B ILE* 1.3 70.0 + - - +
653B VAL* 3.6 13.6 + - + +
678B ILE* 4.5 10.5 - - + -
722B TRP* 3.3 37.5 - - + -
723B LEU 3.3 13.2 - - - +
724B VAL* 4.5 15.7 - - + -
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Residues in contact with ILE 652 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629B LEU* 4.2 9.9 - - + -
640B ILE* 3.9 23.8 - - + -
641B PHE 3.6 4.7 - - - +
642B VAL* 4.2 5.8 - - + -
650B GLU* 5.2 0.9 - - - +
651B ILE* 1.3 73.4 - - - +
653B VAL* 1.3 64.9 + - - +
654B ALA* 4.7 3.6 - - + +
667B PHE* 4.0 12.3 - - + -
669B ILE* 3.8 28.3 - - + -
675B TRP* 3.4 41.5 - - + -
711B LEU* 4.0 11.7 - - + -
713B LEU* 5.8 0.2 - - + -
721B ILE 3.6 1.0 - - - +
722B TRP* 3.2 5.7 - - - -
723B LEU* 2.8 47.3 + - + +
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Residues in contact with VAL 653 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555B GLY 4.7 3.4 - - - +
556B TRP* 5.3 2.0 - - + -
559B ALA* 3.8 24.5 - - + -
616B MET* 4.5 2.2 - - + -
639B LEU 3.8 1.2 - - - +
640B ILE* 3.2 5.5 - - - +
641B PHE* 2.9 63.5 + - + +
643B ARG* 4.8 0.9 - - + -
651B ILE* 3.6 24.9 - - + +
652B ILE* 1.3 79.4 - - - +
654B ALA* 1.3 62.0 + - - +
655B SER* 4.7 10.5 - - - +
720B THR* 5.0 1.3 - - - +
721B ILE 3.5 2.5 - - - +
722B TRP* 3.7 24.9 - - + +
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Residues in contact with ALA 654 (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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639B LEU 3.6 4.0 - - - -
640B ILE* 3.9 19.5 - - + -
652B ILE* 4.1 6.0 - - + -
653B VAL* 1.3 75.6 - - - +
655B SER* 1.3 62.2 + - - +
667B PHE* 5.5 2.5 - - + -
713B LEU* 5.8 0.9 - - + -
715B LEU* 3.7 29.8 - - + +
719B ALA 4.1 0.3 - - - +
720B THR* 3.0 3.1 - - - -
721B ILE* 2.8 46.6 + - + +
723B LEU* 5.8 0.7 - - + -
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Residues in contact with SER 655 (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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556B TRP* 3.6 18.7 - - - +
637B SER 3.8 0.7 - - - +
638B VAL* 3.2 10.9 - - - +
639B LEU 3.0 35.9 + - - -
640B ILE* 4.9 0.2 - - - +
653B VAL* 4.7 3.6 - - - +
654B ALA* 1.3 72.2 - - - +
656B ASN* 1.3 59.9 + - - +
657B PHE* 3.3 30.3 - - - -
715B LEU* 5.2 1.6 - - - -
719B ALA 3.5 4.0 - - - -
720B THR* 2.9 26.6 - - - +
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Residues in contact with ASN 656 (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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636B ARG 4.1 8.7 + - - -
637B SER 3.9 2.0 - - - -
638B VAL* 4.2 5.2 - - + +
655B SER* 1.3 73.0 - - - +
657B PHE* 1.3 60.6 + - - +
658B THR* 3.1 34.8 + - - +
660B VAL 2.8 23.4 + - - +
662B ARG* 3.7 13.2 - - - +
715B LEU* 3.1 28.3 - - + +
716B PRO 3.1 19.5 - - - +
718B LEU* 3.2 22.0 + - - -
719B ALA 2.9 11.1 + - - +
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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