Contacts of the strand formed by residues 650 - 656 (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 GLU 650 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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642A VAL* 3.4 27.6 - - + +
643A ARG 3.0 14.1 - - - +
644A ARG* 2.8 35.8 + - + -
648A GLY 4.3 0.4 - - - +
649A ASN* 1.3 77.3 - - - +
651A ILE* 1.3 65.3 + - - +
670A ASN* 2.9 36.7 + - - +
671A GLN* 2.9 40.4 + - + +
675A TRP* 3.3 26.9 - - + -
724A VAL* 4.8 1.7 - - - +
725A ARG* 4.7 4.5 + - - +
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Residues in contact with ILE 651 (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* 3.7 42.2 - - + +
615A ALA* 4.0 16.4 - - + -
616A MET* 3.8 27.4 - - + -
642A VAL* 3.4 4.4 - - - -
643A ARG* 2.9 28.9 + - + +
650A GLU* 1.3 77.9 - - - +
652A ILE* 1.3 71.8 + - - +
653A VAL* 3.6 5.5 + - + +
678A ILE* 4.0 11.2 - - + -
722A TRP* 4.2 14.8 - - + -
723A LEU 3.3 14.8 - - - +
724A VAL* 4.3 11.0 - - + -
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Residues in contact with ILE 652 (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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629A LEU* 4.4 3.1 - - + -
640A ILE* 3.7 23.8 - - + -
641A PHE 3.8 4.5 - - - +
642A VAL* 4.0 12.3 - - + -
651A ILE* 1.3 74.1 - - - +
653A VAL* 1.3 64.2 + - - +
654A ALA* 4.7 0.9 - - + +
667A PHE* 4.2 9.2 - - + -
669A ILE* 4.0 18.4 - - + -
675A TRP* 3.6 31.9 - - + -
711A LEU* 3.5 30.3 - - + -
722A TRP* 3.1 7.8 - - - -
723A LEU* 2.9 54.3 + - + +
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Residues in contact with VAL 653 (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 5.2 0.7 - - - +
556A TRP* 5.2 4.9 - - + -
559A ALA* 3.7 22.9 - - + -
616A MET* 4.3 10.1 - - + -
639A LEU 3.6 1.6 - - - +
640A ILE* 3.1 6.3 - - - +
641A PHE* 2.8 81.3 + - + +
643A ARG* 4.7 0.9 - - + -
651A ILE* 4.0 10.8 - - + +
652A ILE* 1.3 78.1 - - - +
654A ALA* 1.3 61.3 + - - +
655A SER* 4.8 6.5 - - - +
720A THR* 4.7 6.3 - - - +
721A ILE 3.6 2.7 - - - +
722A TRP* 4.1 15.5 - - + +
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Residues in contact with ALA 654 (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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639A LEU 3.6 3.4 - - - -
640A ILE* 3.9 21.8 - - + -
652A ILE* 4.1 5.3 - - + -
653A VAL* 1.3 74.7 - - - +
655A SER* 1.3 62.3 + - - +
667A PHE* 5.6 0.2 - - + -
713A LEU* 5.5 2.2 - - + -
715A LEU* 3.8 27.9 - - + +
719A ALA 4.0 0.7 - - - +
720A THR* 3.0 3.3 - - - -
721A ILE* 2.8 48.8 + - + +
723A LEU* 5.1 0.4 - - + -
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Residues in contact with SER 655 (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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556A TRP* 3.5 21.6 - - - +
637A SER 3.6 1.6 - - - +
638A VAL* 3.2 8.9 - - - +
639A LEU 3.0 34.8 + - - -
653A VAL* 4.8 2.3 - - - +
654A ALA* 1.3 72.3 - - - +
656A ASN* 1.3 60.0 + - - +
657A PHE* 3.3 29.0 - - - -
715A LEU* 5.4 1.8 - - - -
719A ALA 3.5 4.0 - - - -
720A THR* 2.8 28.1 - - - +
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Residues in contact with ASN 656 (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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636A ARG 3.9 11.5 + - - -
637A SER 3.8 1.6 - - - -
638A VAL* 4.0 6.1 - - + +
655A SER* 1.3 73.4 - - - +
657A PHE* 1.3 67.2 + - - +
658A THR* 3.3 25.2 + - - +
660A VAL 2.8 22.9 + - - +
662A ARG* 3.6 11.7 - - - +
715A LEU* 3.2 21.2 - - + +
716A PRO 3.2 27.1 - - - +
718A LEU* 3.3 5.5 - - - -
719A ALA 2.9 27.3 + - - +
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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