Contacts of the strand formed by residues 638 - 644 (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 VAL 638 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504B HIS* 4.1 1.0 + - - -
630B VAL* 3.9 6.1 - - - +
633B ASP* 3.2 32.4 + - - +
636B ARG* 3.6 25.6 - - + +
637B SER* 1.3 77.2 - - - +
639B LEU* 1.3 65.9 + - - +
640B ILE* 4.1 9.6 - - + -
655B SER 3.2 9.9 - - - +
656B ASN* 4.2 12.1 - - - +
662B ARG* 4.2 11.0 - - + -
665B TYR* 3.7 25.4 - - + +
715B LEU* 3.3 29.6 - - + -
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Residues in contact with LEU 639 (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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492B TYR* 4.3 3.4 - - - +
504B HIS* 3.4 37.0 - - + +
507B LEU* 3.9 22.7 - - + -
508B THR* 3.9 12.6 - - + -
556B TRP* 3.7 35.9 - - + -
628B TRP* 4.2 5.4 - - + -
630B VAL 3.6 6.3 - - - +
637B SER 3.9 6.1 - - - +
638B VAL* 1.3 74.4 - - - +
640B ILE* 1.3 62.1 + - - +
653B VAL 3.8 1.2 - - - +
654B ALA* 3.6 1.2 - - - -
655B SER* 3.0 33.2 + - - +
657B PHE* 3.6 32.5 - - + -
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Residues in contact with ILE 640 (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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628B TRP* 3.7 3.0 - - - -
629B LEU* 2.6 53.5 + - + -
630B VAL* 2.8 31.9 + - + +
638B VAL* 4.1 9.6 - - + -
639B LEU* 1.3 81.2 - - - +
641B PHE* 1.3 60.1 + - - +
652B ILE* 3.9 7.2 - - + -
653B VAL 3.2 9.9 - - - +
654B ALA* 3.9 15.3 - - + -
665B TYR* 3.8 20.4 - - + -
667B PHE* 3.4 44.6 - - + -
715B LEU* 4.4 1.3 - - + -
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Residues in contact with PHE 641 (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* 3.4 47.8 - + - -
559B ALA* 3.4 40.8 - - + -
560B PHE* 4.3 5.4 - + - -
626B PHE* 3.3 41.1 - + + -
627B GLU 3.2 13.5 - - - +
628B TRP* 3.9 8.7 - + + -
629B LEU* 3.8 6.1 - - - +
640B ILE* 1.3 75.5 - - - +
642B VAL* 1.3 70.3 + - - +
643B ARG* 3.8 10.5 - - + -
652B ILE* 3.6 5.7 - - - +
653B VAL* 2.9 51.2 + - + -
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Residues in contact with VAL 642 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626B PHE* 3.4 4.5 - - - -
627B GLU* 2.7 59.5 + - + +
629B LEU* 4.4 9.9 - - + -
641B PHE* 1.3 79.3 - - - +
643B ARG* 1.3 63.8 + - - +
644B ARG* 3.9 20.0 - - + +
650B GLU* 3.3 39.5 - - + +
651B ILE 3.3 21.8 - - - +
652B ILE* 4.1 9.4 - - + +
670B ASN* 4.3 5.2 - - - +
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Residues in contact with ARG 643 (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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559B ALA* 2.8 40.6 + - - +
560B PHE 3.5 3.0 + - - -
561B PRO* 3.3 23.3 - - - +
564B LYS* 4.7 0.4 - - - +
615B ALA* 3.4 24.5 + - + +
616B MET* 3.8 35.6 + - + -
617B HIS 4.6 0.4 - - - +
619B LEU 4.0 2.2 + - - -
620B ASP* 2.8 43.9 + - - +
625B GLY 2.6 24.2 + - - -
626B PHE* 3.8 15.5 - - - -
641B PHE* 3.8 10.5 - - + -
642B VAL* 1.3 79.7 - - - +
644B ARG* 1.3 61.0 + - - +
649B ASN 3.7 0.2 - - - +
650B GLU* 3.0 23.4 - - - -
651B ILE 3.0 12.9 + - - +
653B VAL* 4.8 1.8 - - + -
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Residues in contact with ARG 644 (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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615B ALA* 3.7 11.4 + - - +
619B LEU* 3.4 22.9 + - - +
623B PRO 4.9 0.6 + - - -
624B TYR* 3.1 67.7 + - + +
625B GLY* 3.2 10.3 + - - -
626B PHE 4.5 1.4 + - - -
627B GLU* 2.6 45.8 + - - +
642B VAL* 3.9 6.0 - - + +
643B ARG* 1.3 72.9 - - - +
645B ASP* 1.3 65.8 - - - +
648B GLY 4.2 7.4 - - - +
649B ASN 3.3 7.0 - - - +
650B GLU* 3.2 46.6 + - + -
670B ASN* 3.8 4.2 - - - +
671B GLN* 5.6 0.2 - - - +
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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