Contacts of the strand formed by residues 642 - 647 (chain D) in PDB entry 3E20
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 642 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583D ILE* 3.1 25.1 - - - +
634D PHE* 3.1 32.8 - - + -
638D GLN* 3.0 34.0 + - - +
639D TYR* 3.8 16.1 + - + +
641D GLY* 1.3 79.4 - - - +
643D PHE* 1.3 66.0 + - - +
644D THR* 6.4 0.2 - - + -
655D GLY 3.6 5.8 - - - +
656D LYS* 4.6 4.2 - - + +
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Residues in contact with PHE 643 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560D PHE* 4.0 9.4 - + - -
562D ALA* 3.7 21.1 - - + -
564D ILE* 4.5 5.4 - - + -
581D MET* 3.5 22.0 - - + -
582D HIS 3.3 16.6 - - - +
583D ILE* 3.5 21.5 - - + -
623D LEU* 4.1 8.7 - - + -
641D GLY 3.6 10.3 - - - -
642D ARG* 1.3 77.5 - - - +
644D THR* 1.3 64.5 + - - +
645D LEU* 3.2 35.4 - - + -
654D VAL* 3.5 2.0 - - - +
655D GLY* 2.9 65.2 + - - +
656D LYS 3.6 14.1 - - - -
657D VAL* 3.7 3.4 - - + -
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Residues in contact with THR 644 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580D VAL 3.9 0.3 - - - +
581D MET* 3.5 0.5 - - - +
582D HIS* 3.1 38.8 + - + +
642D ARG* 6.4 0.2 - - + -
643D PHE* 1.3 80.6 - - - +
645D LEU* 1.3 67.7 + - - +
646D ARG* 4.2 13.5 + - - -
651D THR* 4.1 16.3 + - + +
653D ALA 3.5 10.1 - - - -
654D VAL* 4.1 13.2 - - + +
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Residues in contact with LEU 645 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564D ILE* 4.5 8.1 - - + -
579D CYS* 3.7 17.3 - - - -
580D VAL 3.4 2.0 - - - +
581D MET* 3.8 15.9 - - + -
590D VAL* 4.5 3.1 - - + -
592D PHE* 3.8 34.1 - - + -
623D LEU* 4.8 4.3 - - + -
643D PHE* 3.2 42.8 - - + -
644D THR* 1.3 74.6 - - - +
646D ARG* 1.3 67.8 + - - +
651D THR* 3.4 2.6 - - - +
652D VAL* 2.9 36.7 + - + -
653D ALA* 2.7 30.2 + - + +
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Residues in contact with ARG 646 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579D CYS* 3.6 5.0 - - - +
580D VAL* 2.7 36.7 + - - +
582D HIS* 3.2 37.3 + - - +
644D THR* 4.2 8.4 + - - -
645D LEU* 1.3 80.3 - - - +
647D ASP* 1.3 53.4 + - - +
648D GLN* 2.7 44.6 + - + +
650D THR* 3.3 8.3 - - - +
651D THR* 3.5 28.9 + - + +
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Residues in contact with ASP 647 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396C GLN* 3.3 28.7 + - - +
569D LEU* 4.8 1.0 - - - +
570D PRO* 5.1 7.4 - - + +
577D TYR* 2.7 28.3 + - - +
578D SER 5.0 0.5 - - - +
579D CYS* 4.3 6.6 - - - +
646D ARG* 1.3 65.2 - - - +
648D GLN* 1.3 49.6 - - - +
649D GLY* 2.0 26.1 + - - -
650D THR* 3.2 9.3 + - + +
652D VAL* 3.7 19.4 - - + +
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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