Contacts of the strand formed by residues 641 - 646 (chain A) in PDB entry 1D0N
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 ARG 641 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361A LEU* 3.4 34.0 - - - +
364A GLN* 4.3 12.1 + - - +
386A HIS* 4.9 6.5 - - + +
639A PRO* 3.7 14.4 - - + +
640A PRO* 1.3 80.7 - - - +
642A LEU* 1.3 61.8 + - - +
643A PHE* 3.3 35.8 - - + -
656A GLU* 3.0 35.0 + - - +
661A PHE* 3.9 6.5 - - - -
673A LEU 3.5 0.7 - - - +
674A LEU* 3.7 2.9 - - - +
675A ASP* 2.8 40.9 + - + +
703A TYR* 5.2 1.6 + - - -
707A ASP* 5.8 1.8 + - - -
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Residues in contact with LEU 642 (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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641A ARG* 1.3 75.3 - - - +
643A PHE* 1.3 66.3 + - - +
656A GLU* 3.5 8.5 + - - +
657A VAL* 2.9 53.9 + - + +
661A PHE* 3.5 36.1 - - + -
665A ASP* 4.9 5.2 - - + -
666A LEU* 4.3 14.4 - - + -
672A MET* 4.2 15.7 - - + -
673A LEU 3.6 20.4 - - - +
674A LEU* 4.0 15.9 - - + -
729A PHE* 5.8 2.2 - - + -
733A PHE* 4.3 20.9 - - + -
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Residues in contact with PHE 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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641A ARG* 3.3 59.5 - - + -
642A LEU* 1.3 75.7 - - - +
644A ALA* 1.3 64.9 + - - +
654A ILE* 4.2 26.5 - - + -
655A GLU 3.4 7.6 - - - +
656A GLU* 3.5 33.4 - - + -
657A VAL* 4.2 1.1 - - - -
672A MET* 3.4 15.5 - - - +
673A LEU* 3.0 47.1 + - + +
675A ASP* 4.3 2.2 - - + -
703A TYR* 3.3 37.2 - + + -
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Residues in contact with ALA 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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169A ARG* 3.4 39.5 - - - +
643A PHE* 1.3 75.3 - - - +
645A CYS* 1.3 62.4 - - - +
646A SER* 5.1 1.7 + - - +
653A VAL 3.9 0.2 - - - +
654A ILE* 3.3 10.7 - - - +
655A GLU* 2.8 36.6 + - + +
657A VAL* 5.6 0.4 - - + -
670A ASP* 5.1 3.1 - - - +
671A VAL 4.0 2.9 - - - -
672A MET* 4.0 11.7 - - + -
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Residues in contact with CYS 645 (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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644A ALA* 1.3 73.8 - - - +
646A SER* 1.3 67.3 + - - +
647A ASN* 5.4 0.7 - - - +
648A LYS* 6.0 0.2 - - - -
652A PHE* 4.3 12.8 - - + -
653A VAL 4.0 2.0 - - - -
654A ILE* 4.8 2.2 - - - -
670A ASP* 4.5 9.6 + - - +
671A VAL* 2.8 40.4 + - + +
673A LEU* 3.4 44.4 - - - -
692A GLU* 4.6 8.2 - - - +
699A SER* 4.2 20.4 - - - +
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Residues in contact with SER 646 (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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644A ALA* 5.1 2.6 + - - +
645A CYS* 1.3 78.6 + - - +
647A ASN* 1.3 66.1 + - - +
648A LYS* 3.4 26.1 + - - +
651A ARG 3.1 2.5 - - - +
652A PHE* 5.2 0.6 - - - -
653A VAL* 2.7 60.9 + - - +
670A ASP* 5.3 2.1 + - - -
692A GLU* 4.0 5.2 - - - -
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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