Contacts of the helix formed by residues 714 - 726 (chain E) in PDB entry 3RWR
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 LEU 714 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140D MET 5.1 0.9 - - - +
143D SER* 4.1 23.6 - - - +
144D LEU* 3.9 37.9 - - + +
147D GLN* 3.6 18.6 - - - +
642E MET* 4.6 9.0 - - - -
646E LEU* 4.7 1.1 - - + -
710E PHE* 3.8 31.2 - - + +
712E MET 2.5 14.8 + - - -
713E ASN* 1.3 75.6 - - - +
715E GLN* 1.3 65.5 + - - +
716E ASP* 3.1 4.5 - - - +
717E LEU* 2.8 46.1 + - + +
718E TYR* 3.5 2.3 + - - -
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Residues in contact with GLN 715 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512E PRO* 3.1 13.2 - - + +
513E TRP* 2.5 48.0 - - - +
710E PHE* 2.8 40.3 + - - +
711E VAL* 2.9 34.2 - - - +
712E MET 3.3 4.0 + - - +
714E LEU* 1.3 74.4 - - - +
716E ASP* 1.3 63.3 + - - +
718E TYR* 2.8 46.2 + - - +
719E MET* 3.4 6.6 + - - +
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Residues in contact with ASP 716 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194D MET* 6.5 1.6 - - - -
712E MET 4.6 2.9 + - - +
714E LEU 2.8 6.1 + - - +
715E GLN* 1.3 74.6 - - - +
717E LEU* 1.3 63.4 + - - +
719E MET* 3.2 9.3 + - - +
720E ALA* 3.1 21.7 + - - +
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Residues in contact with LEU 717 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194D MET* 4.0 34.7 - - + +
198D LEU* 4.3 14.1 - - + -
642E MET* 3.8 25.4 - - + +
645E ALA* 5.5 0.4 - - + -
646E LEU* 3.2 36.1 - - + +
714E LEU* 2.8 27.8 + - + +
716E ASP* 1.3 74.3 - - - +
718E TYR* 1.3 64.8 + - - +
720E ALA* 2.8 7.4 + - - +
721E VAL* 2.8 49.7 + - + +
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Residues in contact with TYR 718 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509E LEU 4.4 2.4 + - - -
511E GLN 3.5 12.0 + - - -
512E PRO* 3.6 3.8 - - + -
513E TRP* 3.3 29.2 - + - -
526E LYS* 2.8 25.3 + - - -
634E HIS* 3.2 32.3 + - - -
638E PRO* 4.2 14.8 - - + -
639E LEU* 6.1 0.4 - - + -
642E MET* 3.3 32.7 - - + -
710E PHE* 4.0 12.6 - + + -
714E LEU 3.5 1.6 + - - +
715E GLN* 2.8 33.6 + - - +
717E LEU* 1.3 77.5 - - - +
719E MET* 1.3 54.7 + - - +
721E VAL* 3.3 1.9 + - - +
722E THR* 2.8 56.0 + - - +
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Residues in contact with MET 719 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509E LEU 4.3 0.4 - - - +
510E MET* 3.6 39.5 - - + +
511E GLN 4.5 0.4 - - - +
512E PRO* 4.0 34.1 - - + -
715E GLN 3.4 2.7 + - - +
716E ASP* 3.2 12.6 + - - +
718E TYR* 1.3 81.9 - - - +
720E ALA* 1.3 63.1 + - - +
722E THR* 3.2 9.3 + - + -
723E THR* 3.0 46.8 + - - +
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Residues in contact with ALA 720 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194D MET* 5.1 5.6 - - + -
198D LEU* 4.2 23.1 - - + +
716E ASP* 3.1 13.8 + - - +
717E LEU* 2.8 15.2 + - + +
719E MET* 1.3 79.4 - - - +
721E VAL* 1.3 58.0 + - - +
723E THR* 3.0 25.0 - - - +
724E GLN* 3.4 10.2 + - - +
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Residues in contact with VAL 721 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D LEU* 4.9 4.5 - - + -
202D CYS* 3.4 35.0 - - + -
638E PRO* 4.0 13.2 - - - +
641E GLY* 4.0 2.2 - - - -
642E MET* 3.5 21.5 - - + -
717E LEU* 2.8 40.0 + - + +
718E TYR 3.8 2.7 - - - +
720E ALA* 1.3 69.7 - - + +
722E THR* 1.3 65.8 + - - +
724E GLN* 3.2 14.9 + - - +
725E HIS* 3.3 34.1 + - + +
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Residues in contact with THR 722 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509E LEU* 3.2 50.0 - - + +
510E MET* 4.8 0.2 - - - -
633E GLN 5.0 2.7 - - - +
638E PRO* 4.0 10.3 - - + +
718E TYR* 2.8 49.8 + - + +
719E MET* 3.2 13.0 + - + -
721E VAL* 1.3 77.9 - - - +
723E THR* 1.3 63.2 + - - +
724E GLN 3.1 1.0 + - - -
725E HIS* 3.4 11.7 + - - +
726E HIS* 3.7 13.4 + - - +
727E HIS 4.2 2.8 + - - +
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Residues in contact with THR 723 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510E MET* 5.3 2.6 - - - +
719E MET* 3.0 30.3 + - - +
720E ALA* 3.0 25.4 - - - +
722E THR* 1.3 75.0 - - - +
724E GLN* 1.3 62.3 + - + +
726E HIS 4.2 0.5 - - - +
727E HIS* 2.9 38.2 - - - -
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Residues in contact with GLN 724 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D LEU* 6.3 2.0 - - + -
199D PRO* 3.5 39.3 - - + +
202D CYS* 4.2 19.3 - - - -
720E ALA 3.7 10.0 + - - +
721E VAL* 3.2 13.0 + - - +
722E THR 3.0 0.4 - - - -
723E THR* 1.3 82.9 - - - +
725E HIS* 1.3 75.2 + - + +
726E HIS 4.0 1.9 - - - +
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Residues in contact with HIS 725 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D CYS* 3.5 27.6 + - - -
203D SER* 5.1 2.9 - - - -
204D ILE* 4.6 7.1 + - + +
637E ARG* 4.1 23.6 + - - +
638E PRO* 3.8 34.4 - - + +
641E GLY* 4.5 1.1 - - - -
721E VAL* 3.3 28.4 + - + +
722E THR* 3.4 4.2 + - - +
724E GLN* 1.3 88.0 - - + +
726E HIS* 1.3 83.7 + - + +
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Residues in contact with HIS 726 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509E LEU* 3.6 31.2 - - + +
633E GLN* 3.4 46.1 + - + +
637E ARG* 4.7 15.3 + - + -
638E PRO* 5.8 2.0 - - + -
722E THR* 3.7 5.4 + - + +
723E THR 4.2 1.2 - - - +
724E GLN 4.0 3.1 - - - +
725E HIS* 1.3 103.0 - - + +
727E HIS* 1.3 64.4 + - + +
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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