Contacts of the strand formed by residues 719 - 726 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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552A ALA* 3.5 6.7 - - - +
654A ALA 4.0 0.7 - - - +
655A SER* 3.5 0.3 - - - -
656A ASN* 2.9 32.4 + - - +
680A ASN* 4.7 1.6 - - - +
681A THR* 3.0 20.4 - - - +
682A ASP* 3.9 23.8 - - + +
716A PRO* 3.8 14.1 + - + +
717A PRO 3.2 9.6 - - - +
718A LEU* 1.3 78.8 - - - +
720A THR* 1.3 63.3 + - - +
721A ILE* 5.5 0.7 - - - -
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Residues in contact with THR 720 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552A ALA* 2.7 37.9 - - + +
555A GLY* 3.7 11.9 - - - -
556A TRP 3.9 5.2 - - - +
653A VAL* 4.7 2.8 - - - +
654A ALA 3.0 6.3 - - - -
655A SER* 2.8 30.2 + - - +
657A PHE* 4.7 0.2 - - + -
679A LEU* 4.0 2.1 - - - +
680A ASN* 3.8 0.5 - - - -
681A THR* 3.2 30.7 + - - +
719A ALA* 1.3 76.9 - - - +
721A ILE* 1.3 64.9 + - - +
722A TRP* 3.7 19.6 + - - -
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Residues in contact with ILE 721 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652A ILE 3.7 0.2 - - - +
653A VAL* 3.6 0.5 - - - -
654A ALA* 2.8 42.4 + - + +
677A GLU* 4.1 5.8 - - - +
679A LEU 3.0 8.7 - - - +
680A ASN* 3.7 32.5 - - + +
693A ASN* 4.1 18.4 - - - +
713A LEU* 4.2 10.1 - - + -
714A THR 4.4 1.3 - - - +
715A LEU* 4.3 14.4 - - + -
716A PRO* 3.9 17.9 - - + -
720A THR* 1.3 77.2 - - - +
722A TRP* 1.3 70.9 + - - +
723A LEU* 3.7 32.8 - - + -
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Residues in contact with TRP 722 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555A GLY 3.4 27.3 + - - -
558A TRP* 3.8 23.1 - - + -
559A ALA* 3.6 21.9 - - + +
606A LEU* 4.5 12.3 - - + -
609A THR* 3.8 37.0 - - + -
610A TYR* 4.1 8.7 - - - -
616A MET* 4.0 26.9 - - + -
651A ILE* 4.2 3.6 - - + -
652A ILE 3.1 7.4 - - - +
653A VAL* 4.1 13.4 - - + +
677A GLU* 3.2 0.9 - - - -
678A ILE* 2.8 43.0 + - + -
679A LEU* 2.8 31.2 + - + +
720A THR* 3.7 10.4 + - - -
721A ILE* 1.3 87.3 - - - +
723A LEU* 1.3 67.5 + - - +
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Residues in contact with LEU 723 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651A ILE* 3.3 11.0 - - - +
652A ILE* 2.9 62.6 + - + +
654A ALA* 5.1 1.3 - - + -
675A TRP* 3.5 25.2 - - + -
676A ARG 3.2 8.5 - - - +
677A GLU* 3.3 35.2 - - + +
678A ILE* 4.3 1.6 - - - -
693A ASN* 5.5 1.1 - - + +
713A LEU* 4.1 17.9 - - + -
721A ILE* 3.7 28.0 - - + +
722A TRP* 1.3 87.3 - - - +
724A VAL* 1.3 60.8 + - - +
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Residues in contact with VAL 724 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613A HIS* 4.1 21.8 - - + +
650A GLU 5.0 1.8 - - - +
651A ILE* 4.3 12.3 - - + -
675A TRP* 3.3 8.5 - - - -
676A ARG* 2.9 39.3 + - + +
678A ILE* 3.5 33.1 - - + +
723A LEU* 1.3 73.9 - - - +
725A ARG* 1.3 74.3 + - - +
726A GLU* 3.8 5.5 + - + +
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Residues in contact with ARG 725 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650A GLU 4.7 1.7 + - - +
671A GLN* 3.6 31.3 + - - +
672A PRO 2.6 27.3 + - - -
673A GLY* 4.1 7.7 - - - -
674A LYS 3.2 13.9 - - - +
675A TRP* 3.4 25.3 - - + +
724A VAL* 1.3 88.6 - - - +
726A GLU* 1.3 77.6 + - - +
727A ALA* 3.8 13.2 + - - +
728A GLU* 4.6 10.5 + - - +
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Residues in contact with GLU 726 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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674A LYS* 2.7 41.6 + - + +
676A ARG* 2.6 47.8 + - + +
696A THR* 3.3 17.8 + - - -
724A VAL* 4.9 6.3 - - + +
725A ARG* 1.3 83.9 + - - +
727A ALA* 1.3 67.2 + - - +
728A GLU* 3.6 12.6 - - - +
254B ARG* 6.0 3.6 - - - -
590B GLU* 3.6 12.5 - - - +
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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