Contacts of the strand formed by residues 638 - 644 (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 VAL 638 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504A HIS* 4.0 1.9 + - - -
630A VAL* 4.2 4.4 - - + +
633A ASP* 3.3 28.0 + - - +
636A ARG* 3.8 16.4 - - + +
637A SER* 1.3 82.1 - - - +
639A LEU* 1.3 65.7 + - - +
640A ILE* 4.1 10.8 - - + -
655A SER 3.2 7.2 - - - +
656A ASN* 4.0 14.6 - - - +
662A ARG* 4.4 5.8 - - + -
665A TYR* 3.5 34.5 - - + +
715A LEU* 3.4 34.5 - - + -
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Residues in contact with LEU 639 (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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492A TYR* 4.5 1.6 - - - +
504A HIS* 3.7 26.7 - - + +
507A LEU* 3.9 28.5 - - + -
508A THR* 3.7 30.3 - - + -
556A TRP* 3.8 31.4 - - + -
628A TRP* 4.3 8.1 - - + -
630A VAL 3.6 6.5 - - - +
631A VAL 5.0 0.7 - - - +
637A SER 4.1 4.9 - - - +
638A VAL* 1.3 77.7 - - - +
640A ILE* 1.3 62.7 + - - +
653A VAL 3.6 1.6 - - - +
654A ALA* 3.6 1.2 - - - -
655A SER* 3.0 32.5 + - - -
657A PHE* 3.9 19.1 - - + -
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Residues in contact with ILE 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628A TRP* 3.4 4.0 - - - -
629A LEU* 2.9 31.3 + - + -
630A VAL* 2.9 35.1 + - + +
638A VAL* 4.1 9.2 - - + -
639A LEU* 1.3 79.4 - - - +
641A PHE* 1.3 65.8 + - - +
652A ILE* 3.7 24.7 - - + -
653A VAL 3.1 15.5 - - - +
654A ALA* 3.9 13.9 - - + -
665A TYR* 3.8 14.1 - - + -
667A PHE* 3.4 39.7 - - + -
715A LEU* 4.8 1.1 - - + -
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Residues in contact with PHE 641 (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* 4.0 28.9 - + - -
559A ALA* 3.4 31.0 - - + -
560A PHE* 4.2 8.1 - + - -
626A PHE* 3.3 42.2 - + + -
627A GLU 3.3 14.8 - - - +
628A TRP* 3.6 18.4 - + + -
629A LEU* 3.8 7.2 - - - +
640A ILE* 1.3 76.2 - - - +
642A VAL* 1.3 70.0 + - - +
643A ARG* 3.8 8.3 - - + -
652A ILE* 3.7 1.6 - - - -
653A VAL* 2.8 65.8 + - + -
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Residues in contact with VAL 642 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625A GLY 5.5 0.2 - - - +
626A PHE* 3.6 5.2 - - - -
627A GLU* 2.8 32.9 + - + +
629A LEU* 4.1 18.1 - - + +
641A PHE* 1.3 82.7 - - - +
643A ARG* 1.3 66.1 + - - +
644A ARG* 4.6 10.5 - - + +
650A GLU* 3.4 51.6 - - + +
651A ILE 3.4 11.9 - - - +
652A ILE* 4.0 23.1 - - + -
670A ASN* 4.7 2.9 - - - +
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Residues in contact with ARG 643 (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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559A ALA 3.0 23.9 + - - +
560A PHE 3.3 9.5 + - - -
561A PRO* 3.1 32.7 - - - +
564A LYS* 4.9 1.4 - - - +
615A ALA* 3.4 29.7 + - + +
616A MET* 3.8 37.5 + - + -
617A HIS 4.4 0.8 - - - +
619A LEU 4.3 5.3 + - - +
620A ASP* 2.6 41.2 + - - +
625A GLY* 3.1 16.9 + - - -
626A PHE* 4.3 8.5 - - - -
641A PHE* 3.8 10.3 - - + -
642A VAL* 1.3 75.3 - - - +
644A ARG* 1.3 61.9 + - - +
649A ASN 3.7 0.2 - - - +
650A GLU* 3.0 7.6 - - - +
651A ILE 2.9 32.9 + - - +
653A VAL* 4.7 0.2 - - + -
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Residues in contact with ARG 644 (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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615A ALA* 3.8 10.1 + - - +
619A LEU* 3.6 9.2 + - - +
623A PRO 5.0 0.4 + - - -
624A TYR* 2.8 61.5 + - + +
625A GLY* 3.0 24.3 + - - +
626A PHE 4.6 1.8 + - - -
627A GLU* 3.1 39.3 + - - +
642A VAL* 4.6 4.2 - - + +
643A ARG* 1.3 77.9 + - - +
645A ASP* 1.3 75.3 + - - +
648A GLY* 3.7 13.7 - - - -
649A ASN 3.3 11.9 - - - +
650A GLU* 2.8 33.0 + - + -
670A ASN* 4.2 4.0 - - - +
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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