Contacts of the helix formed by residues 640 - 648 (chain B) in PDB entry 2R5N
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 PRO 640 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A ARG 3.8 9.4 - - - +
92A GLN* 3.8 21.3 - - - +
468B GLU* 3.6 25.5 - - + +
639B ALA* 1.4 91.3 - - + +
641B ALA* 1.3 66.5 + - - +
642B GLU* 4.6 5.4 - - + +
643B LEU* 3.1 28.5 + - + +
644B LEU* 3.1 18.0 + - - +
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Residues in contact with ALA 641 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464B ILE 4.1 10.3 - - - -
465B GLY* 3.3 35.4 - - - +
466B LEU 4.9 0.2 - - - -
467B GLY* 3.8 7.3 - - - -
468B GLU* 4.7 0.8 + - - -
521B GLN* 5.5 4.9 - - + -
639B ALA 3.6 2.0 + - - -
640B PRO* 1.3 69.9 - - - +
642B GLU* 1.3 65.2 + - - +
644B LEU* 3.0 5.0 + - - +
645B PHE* 2.9 34.0 + - + -
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Residues in contact with GLU 642 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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640B PRO* 3.3 3.7 - - + +
641B ALA* 1.3 78.8 - - - +
643B LEU* 1.3 74.3 + - + +
645B PHE* 3.5 8.7 + - - +
646B GLU* 3.2 21.9 + - + +
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Residues in contact with LEU 643 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A GLN* 5.2 3.8 - - - +
93A LEU* 4.9 16.5 - - + +
639B ALA* 4.9 6.7 - - + -
640B PRO* 3.1 34.4 + - + +
642B GLU* 1.3 86.8 - - + +
644B LEU* 1.3 60.8 + - - +
646B GLU* 3.4 20.0 + - - +
647B GLU* 2.8 31.0 + - - +
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Residues in contact with LEU 644 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A LEU* 4.1 6.7 - - + -
464B ILE* 3.5 33.7 - - + +
467B GLY* 3.9 2.2 - - - +
474B GLN* 3.2 30.3 - - - +
637B GLU* 3.3 32.1 - - + +
639B ALA* 3.4 32.5 - - + +
640B PRO 3.1 12.6 + - - +
641B ALA 3.0 7.0 + - - +
643B LEU* 1.3 74.5 - - - +
645B PHE* 1.3 65.4 + - - +
647B GLU* 3.2 2.8 + - + -
648B PHE* 2.9 39.0 + - + +
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Residues in contact with PHE 645 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463B SER* 4.1 2.9 - - - -
464B ILE* 3.7 25.1 - - + -
465B GLY* 3.5 33.4 - - - -
521B GLN* 3.8 17.5 - - + -
559B SER* 4.5 0.2 - - - -
560B GLU* 3.6 11.9 - - - -
613B ALA* 4.0 8.3 - - + -
641B ALA* 2.9 30.9 + - + +
642B GLU* 3.9 7.0 - - - +
644B LEU* 1.3 75.5 - - - +
646B GLU* 1.3 61.6 + - - +
648B PHE 3.5 0.5 + - - -
649B GLY 3.2 4.2 + - - -
650B PHE* 2.8 39.9 + + + +
677B EDO 3.6 49.1 - - - +
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Residues in contact with GLU 646 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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642B GLU* 3.2 12.0 + - + +
643B LEU* 3.6 27.3 - - - +
644B LEU 3.2 0.2 - - - -
645B PHE* 1.3 78.9 - - - +
647B GLU* 1.3 64.0 + - - +
649B GLY* 3.2 13.2 + - - -
651B THR* 3.9 23.5 - - + +
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Residues in contact with GLU 647 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A LEU* 3.8 25.2 - - + +
94A HIS* 3.6 28.2 + - - +
637B GLU* 5.7 1.5 - - + +
643B LEU 2.8 20.8 + - - +
644B LEU* 3.6 7.4 - - - +
646B GLU* 1.3 74.3 - - - +
648B PHE* 1.3 79.8 + - + +
649B GLY 3.3 0.9 + - - -
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Residues in contact with PHE 648 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464B ILE* 3.9 13.9 - - + -
630B VAL* 5.6 1.2 - - - +
631B GLY 4.3 8.0 - - - +
632B MET* 3.6 31.6 - - + -
633B THR 6.2 0.4 - - - -
634B THR* 3.3 24.0 - - + -
635B PHE 3.6 16.2 - - - -
636B GLY* 4.0 8.7 - - - -
637B GLU* 4.0 20.2 - - + -
644B LEU* 2.9 43.9 + - + +
647B GLU* 1.3 88.0 - - + +
649B GLY* 1.3 59.5 + - - +
650B PHE* 3.5 19.4 + - + -
654B ASN* 5.2 0.3 + - - -
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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