Contacts of the helix formed by residues 644 - 653 (chain A) in PDB entry 4RH5
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 GLY 644 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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640A GLY 3.0 7.0 + - - -
641A LEU 3.7 5.2 + - - -
642A GLU 3.5 1.6 - - - -
643A SER* 1.3 77.8 - - - +
645A THR* 1.3 63.3 + - - +
646A VAL* 3.3 2.9 - - - -
647A LEU* 3.3 13.2 + - - +
648A ILE* 3.1 28.9 + - - +
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Residues in contact with THR 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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640A GLY* 3.2 18.2 + - - -
643A SER* 3.6 16.7 + - - +
644A GLY* 1.3 76.2 - - - +
646A VAL* 1.3 69.6 + - - +
648A ILE* 3.3 8.0 + - - +
649A GLN* 3.0 35.0 + - - +
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Residues in contact with VAL 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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636A GLN* 4.7 3.6 - - + +
637A LEU* 4.1 24.5 - - + +
640A GLY* 3.4 31.4 - - - +
641A LEU* 3.6 31.0 - - + +
644A GLY* 5.1 0.7 - - - -
645A THR* 1.3 79.0 + - - +
647A LEU* 1.3 72.2 + - + +
649A GLN* 3.5 6.8 + - - +
650A PHE* 3.1 21.7 + - - +
871A LEU* 5.4 0.2 - - - +
891A TYR* 3.7 19.3 + - + +
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Residues in contact with LEU 647 (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 LEU* 4.9 1.1 - - + -
644A GLY* 3.3 11.8 + - - +
645A THR 3.2 0.4 - - - -
646A VAL* 1.3 93.1 - - + +
648A ILE* 1.3 69.7 + - + +
650A PHE* 3.3 6.4 + - + +
651A GLU* 3.0 27.2 + - + +
888A SER* 4.5 21.1 - - - +
891A TYR* 4.3 11.7 - - + -
892A LYS* 4.0 48.9 - - + +
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Residues in contact with ILE 648 (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 GLY* 3.1 20.0 + - - +
645A THR* 3.3 8.7 + - - +
647A LEU* 1.3 79.7 - - + +
649A GLN* 1.3 65.8 + - + +
651A GLU* 3.1 9.2 + - + +
652A GLN* 3.0 42.8 + - + +
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Residues in contact with GLN 649 (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 GLN* 5.8 3.2 - - - +
645A THR* 3.0 26.9 + - - +
646A VAL* 4.0 5.9 - - - +
648A ILE* 1.3 77.9 - - + +
650A PHE* 1.3 62.0 + - - +
652A GLN* 3.3 20.7 + - - +
653A LEU* 3.2 21.0 + - - +
871A LEU* 3.7 31.0 - - + +
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Residues in contact with PHE 650 (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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646A VAL 3.1 5.8 + - - +
647A LEU* 3.5 9.0 - - - +
649A GLN* 1.3 78.0 - - - +
651A GLU* 1.3 77.0 + - + +
653A LEU* 3.2 19.0 + - + +
871A LEU* 3.8 12.0 - - + +
874A VAL* 4.3 11.4 - - + -
878A ARG* 3.5 34.2 + - - -
885A VAL* 3.8 15.3 - - + -
886A GLN 4.6 3.6 - - - -
887A THR 3.8 12.3 - - - -
888A SER* 3.8 30.1 - - - -
891A TYR* 3.4 57.2 - + + -
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Residues in contact with GLU 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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647A LEU* 3.0 19.2 + - + +
648A ILE* 3.1 8.7 + - + +
650A PHE* 1.3 89.2 - - + +
652A GLN* 1.3 61.3 + - + +
653A LEU 3.6 4.7 + - - +
888A SER* 3.8 25.9 + - - -
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Residues in contact with GLN 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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648A ILE* 3.0 31.1 + - + +
649A GLN* 3.6 28.2 + - - +
650A PHE 3.2 0.4 - - - -
651A GLU* 1.3 77.1 - - + +
653A LEU* 1.3 64.0 + - - +
654A TYR* 3.4 1.9 + - - -
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Residues in contact with LEU 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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649A GLN 3.2 11.0 + - - +
650A PHE* 3.2 16.0 + - + +
651A GLU 3.9 5.9 - - - +
652A GLN* 1.3 78.5 - - - +
654A TYR* 1.3 86.5 + - + +
655A ARG* 3.6 4.2 + - - +
871A LEU* 3.7 19.5 - - + +
874A VAL* 3.7 30.5 - - + -
875A ARG* 3.7 52.5 - - + +
878A ARG* 3.8 14.4 + - - +
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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