Contacts of the strand formed by residues 719 - 726 (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 ALA 719 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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551B ARG* 5.7 0.4 - - - +
552B ALA* 3.3 7.4 - - - +
654B ALA 4.1 0.3 - - - +
655B SER* 3.5 0.5 - - - -
656B ASN* 2.9 31.8 + - - +
680B ASN* 4.7 1.1 - - - +
681B THR* 3.0 21.8 - - - +
682B ASP* 3.8 23.8 - - + +
716B PRO* 3.8 12.0 + - + +
717B PRO 3.3 9.8 - - - +
718B LEU* 1.3 79.5 - - - +
720B THR* 1.3 63.8 + - - +
721B ILE* 5.4 1.1 - - - -
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Residues in contact with THR 720 (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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552B ALA* 2.7 35.4 - - + +
555B GLY* 3.4 25.1 + - - -
556B TRP* 4.0 3.6 - - + +
653B VAL* 5.1 2.9 - - - -
654B ALA 3.0 7.2 - - - -
655B SER* 2.9 29.6 - - - +
657B PHE* 4.7 0.9 - - + -
679B LEU* 4.3 1.6 - - - +
680B ASN* 3.7 0.3 - - - -
681B THR* 3.1 29.2 + - - +
719B ALA* 1.3 78.9 - - - +
721B ILE* 1.3 66.5 + - - +
722B TRP* 4.1 6.4 + - - -
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Residues in contact with ILE 721 (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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652B ILE 3.6 1.0 - - - +
653B VAL* 3.5 0.9 - - - -
654B ALA* 2.8 45.4 + - + +
677B GLU* 3.9 6.3 - - - +
679B LEU 3.0 8.5 - - - +
680B ASN* 3.3 34.1 - - + +
693B ASN* 3.9 18.6 - - - +
713B LEU* 4.6 3.6 - - + -
714B THR 4.0 3.4 - - - +
715B LEU* 3.9 24.5 - - + -
716B PRO* 4.0 14.8 - - + -
720B THR* 1.3 79.5 - - - +
722B TRP* 1.3 68.0 + - - +
723B LEU* 3.5 23.6 - - + -
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Residues in contact with TRP 722 (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 3.3 27.9 + - - -
558B TRP* 3.9 24.9 - - + -
559B ALA* 3.7 20.9 - - + +
606B LEU* 4.0 16.2 - - + -
609B THR* 3.9 36.1 - - + -
610B TYR* 4.1 9.4 - - + -
616B MET* 3.7 28.5 - - + -
651B ILE* 3.3 13.0 - - + -
652B ILE 3.2 3.8 - - - -
653B VAL* 3.7 15.5 - - + +
677B GLU* 3.2 5.4 - - - -
678B ILE* 2.8 42.9 + - + -
679B LEU* 2.7 33.3 + - + +
720B THR* 4.1 2.3 + - - -
721B ILE* 1.3 82.4 - - - +
723B LEU* 1.3 58.3 + - - +
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Residues in contact with LEU 723 (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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651B ILE* 3.3 9.0 - - - +
652B ILE* 2.8 45.8 + - + +
654B ALA* 5.8 0.7 - - + -
675B TRP* 3.7 24.8 - - + +
676B ARG* 3.0 30.3 - - - +
677B GLU* 3.7 14.6 - - + +
678B ILE* 4.7 0.9 - - - -
693B ASN* 5.1 3.8 - - + +
697B VAL* 5.9 0.7 - - + -
711B LEU* 5.1 1.3 - - + -
713B LEU* 4.2 28.3 - - + -
721B ILE* 3.5 34.8 - - + +
722B TRP* 1.3 83.1 - - - +
724B VAL* 1.3 61.5 + - - +
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Residues in contact with VAL 724 (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* 4.3 20.6 - - + -
650B GLU 5.3 1.8 - - - +
651B ILE* 4.5 13.7 - - + +
675B TRP* 3.1 8.8 - - - -
676B ARG* 2.6 45.6 + - + +
678B ILE* 3.3 30.9 - - + +
723B LEU* 1.3 75.2 - - - +
725B ARG* 1.3 73.5 + - - +
726B GLU* 3.8 5.4 + - + +
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Residues in contact with ARG 725 (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 4.7 2.8 + - - +
671B GLN* 3.7 26.7 - - - +
672B PRO 2.7 33.5 + - - -
673B GLY* 3.9 7.1 - - - -
674B LYS 3.3 12.1 - - - +
675B TRP* 3.6 30.8 - - + +
724B VAL* 1.3 86.6 - - - +
726B GLU* 1.3 74.4 + - - +
727B ALA* 3.8 10.0 + - - +
728B GLU* 4.0 18.0 + - - +
498D VAL* 3.6 29.0 + - - +
499D TYR* 4.1 5.5 - - - -
501D GLN* 5.7 1.8 + - - -
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Residues in contact with GLU 726 (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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590A GLU* 5.1 3.5 - - - +
674B LYS* 2.8 48.3 + - + +
676B ARG* 2.8 50.2 + - + +
696B THR* 3.6 10.5 + - - +
724B VAL* 3.8 4.7 + - + +
725B ARG* 1.3 86.5 + - - +
727B ALA* 1.3 69.3 + - - +
728B GLU* 3.7 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