Contacts of the helix formed by residues 477 - 484 (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 GLU 477 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442A ARG* 5.0 2.1 + - - +
446A ARG* 2.7 45.2 + - - +
481A SER* 4.9 1.6 - - - +
484A VAL* 3.4 34.5 - - + +
485A THR* 3.6 30.2 + - - +
486A PRO* 3.8 11.2 - - + +
439B GLU* 4.3 4.9 - - - +
476B VAL* 1.3 75.6 - - - +
478B GLN* 1.3 75.6 + - - +
479B VAL 3.4 2.5 - - - -
480B ALA* 3.6 6.5 + - - +
481B SER* 3.3 20.1 + - - -
615B ILE* 4.0 11.7 - - + -
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Residues in contact with GLN 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A ARG* 3.3 12.9 - - - +
435B LEU* 4.2 27.1 - - + +
436B MET* 3.6 13.5 - - - +
438B VAL* 4.2 12.1 - - + +
439B GLU* 2.8 43.9 + - + +
442B ARG* 5.5 0.3 + - - -
475B PRO* 3.1 8.2 - - + +
476B VAL 2.9 24.9 + - - -
477B GLU* 1.3 95.6 - - - +
479B VAL* 1.3 66.0 + - - +
481B SER* 3.2 9.4 + - - -
482B LEU* 3.1 26.3 + - - +
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Residues in contact with VAL 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B LEU* 3.7 26.4 - - + +
462B ASP 5.1 3.1 - - - +
475B PRO* 5.7 0.9 - - + +
476B VAL 4.9 4.6 + - - +
477B GLU 3.4 0.2 - - - -
478B GLN* 1.3 76.6 - - - +
480B ALA* 1.3 56.3 - - - +
482B LEU* 3.0 10.9 + - - +
483B ARG* 2.9 67.3 + - + +
490B THR* 4.2 12.3 - - + -
492B ARG* 5.1 6.5 - - + +
517B ILE* 3.8 23.1 - - + -
612B GLU* 4.8 5.4 - - - +
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Residues in contact with ALA 480 (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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484A VAL* 4.7 9.6 - - + -
476B VAL 5.4 0.8 + - - +
477B GLU 3.6 5.9 + - - +
478B GLN 3.3 0.4 - - - -
479B VAL* 1.3 77.9 - - - +
481B SER* 1.3 62.2 + - - +
483B ARG* 3.3 14.6 + - - +
484B VAL* 3.3 22.5 + - - +
615B ILE* 3.7 30.1 - - + -
618B TYR* 3.8 28.7 - - + -
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Residues in contact with SER 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A GLU* 5.0 3.1 + - - +
481A SER* 3.7 32.6 + - - +
484A VAL* 5.5 2.0 - - - +
442B ARG* 3.0 27.1 + - - -
477B GLU* 3.3 8.9 + - - -
478B GLN* 3.2 12.0 + - - -
479B VAL 3.2 0.6 - - - -
480B ALA* 1.3 80.4 - - - +
482B LEU* 1.3 58.7 + - - +
484B VAL* 3.4 19.4 - - - +
485B THR* 2.9 17.8 + - - -
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Residues in contact with LEU 482 (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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435B LEU* 4.3 13.2 - - + -
438B VAL* 4.5 10.5 - - + -
442B ARG* 3.9 19.3 - - - +
445B VAL* 3.9 28.5 - - + -
459B TYR* 4.4 5.6 - - + -
478B GLN 3.1 17.3 + - - +
479B VAL* 3.0 8.5 + - - +
481B SER* 1.3 74.6 - - - +
483B ARG* 1.3 64.2 + - - +
485B THR* 3.1 16.9 + - - -
488B MET* 3.5 24.6 - - + +
490B THR* 3.5 15.3 - - + +
515B ALA* 4.0 21.3 - - + -
517B ILE* 4.1 19.1 - - + -
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Residues in contact with ARG 483 (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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617A ASP* 4.7 5.9 - - - +
479B VAL* 2.9 44.6 + - + +
480B ALA* 3.3 9.5 + - - +
482B LEU* 1.3 76.2 - - - +
484B VAL* 1.3 61.5 + - - +
485B THR 3.3 3.7 + - - +
488B MET 5.5 2.3 - - - +
490B THR* 4.3 17.6 + - - +
492B ARG* 4.6 8.9 - - - +
557B THR* 3.9 10.9 + - - +
583B MET 5.0 1.6 + - - -
584B PRO 5.6 1.4 + - - -
586B THR* 3.4 27.8 + - - +
587B ASP* 5.7 5.7 - - - +
612B GLU* 2.7 43.0 + - - -
618B TYR* 3.4 44.7 + - + +
619B TRP* 3.7 19.1 - - - -
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Residues in contact with VAL 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A GLU* 3.6 22.0 - - + +
480A ALA* 4.8 7.6 - - + -
481A SER 5.7 1.3 - - - +
615A ILE* 3.4 39.1 - - + +
617A ASP* 4.0 27.4 - - + +
618A TYR* 5.1 3.4 - - - +
480B ALA 3.3 14.1 + - - +
481B SER* 3.4 17.9 - - - +
483B ARG* 1.3 78.8 - - - +
485B THR* 1.3 60.8 + - - +
486B PRO* 3.4 5.4 - - - +
618B TYR* 4.1 16.6 - - + -
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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