Contacts of the helix formed by residues 673 - 687 (chain B) in PDB entry 4RG7
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 GLN 673 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517B GLU 4.6 14.9 - - - +
671B ASN* 3.3 11.6 + - - +
672B PRO* 1.3 81.6 - - + +
674B SER* 1.3 63.5 + - - +
675B SER* 3.1 5.2 + - - -
676B VAL* 3.2 26.3 + - + +
677B LEU* 4.1 2.6 + - - +
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Residues in contact with SER 674 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641B TYR* 3.5 28.2 - - - -
645B TYR* 4.8 12.8 - - - -
667B ALA* 3.6 9.0 + - - -
668B LEU* 4.2 6.0 - - - +
671B ASN* 2.3 46.6 + - - +
672B PRO 3.3 3.6 + - - -
673B GLN* 1.3 74.1 - - - +
675B SER* 1.3 62.5 + - - +
676B VAL 3.4 0.2 + - - -
677B LEU* 3.4 6.4 + - - +
678B LEU* 3.1 24.9 + - - +
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Residues in contact with SER 675 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645B TYR* 6.4 0.4 - - - -
664B PHE* 6.2 0.2 - - - -
668B LEU* 4.1 19.3 - - - +
672B PRO 5.6 0.9 - - - -
673B GLN 3.1 1.3 + - - -
674B SER* 1.3 78.3 - - - +
676B VAL* 1.3 57.7 + - - +
678B LEU* 3.1 3.5 + - - -
679B CYS* 2.6 44.6 + - - -
713B PHE* 5.7 0.7 - - - +
714B HIS* 5.0 8.5 - - - +
717B SER* 3.6 28.7 + - - -
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Residues in contact with VAL 676 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519B SER* 4.0 25.6 - - - -
673B GLN* 3.2 18.5 + - + +
675B SER* 1.3 77.7 - - - +
677B LEU* 1.3 61.9 + - - +
679B CYS* 4.3 3.6 - - - +
680B HIS* 3.1 25.8 + - + +
717B SER* 5.9 2.5 - - - +
720B PHE* 4.8 23.3 - - + -
721B ALA* 5.4 1.7 - - - +
751B LYS* 6.0 3.1 - - + -
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Residues in contact with LEU 677 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516B PHE 5.3 8.7 - - - +
519B SER* 5.7 5.2 - - - -
641B TYR* 4.8 15.3 - - + +
673B GLN 4.1 2.6 + - - +
674B SER* 3.4 10.1 + - - +
675B SER 3.2 0.4 - - - -
676B VAL* 1.3 80.3 - - + +
678B LEU* 1.3 63.7 + - - +
680B HIS* 3.2 7.4 + - - +
681B ILE* 3.1 21.1 + - - +
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Residues in contact with LEU 678 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641B TYR* 6.0 3.6 - - + -
645B TYR* 4.8 18.4 - - + -
646B GLY* 5.8 1.8 - - - +
674B SER* 3.1 18.9 + - - +
675B SER* 3.9 2.7 - - - +
677B LEU* 1.3 78.3 - - - +
679B CYS* 1.3 62.3 + - - +
681B ILE* 3.4 20.9 - - - +
682B GLY* 3.7 4.0 + - - -
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Residues in contact with CYS 679 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675B SER* 2.6 34.2 + - - +
676B VAL* 4.3 3.1 - - - +
678B LEU* 1.3 71.4 - - - +
680B HIS* 1.3 64.3 + - - +
682B GLY* 3.4 9.4 + - - -
683B VAL* 3.5 7.8 + - - +
714B HIS* 4.3 7.6 - - - -
717B SER* 3.6 31.2 - - - +
718B VAL* 3.7 16.3 - - + +
721B ALA* 3.6 27.9 - - + +
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Residues in contact with HIS 680 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519B SER* 6.3 2.7 - - - -
550B TRP* 5.8 0.6 - - - -
551B HIS* 3.9 39.6 + - + +
676B VAL* 3.1 22.6 + - + +
677B LEU* 3.2 8.7 + - - +
679B CYS* 1.3 75.5 - - - +
681B ILE* 1.3 67.1 + - - +
683B VAL* 3.0 19.7 + - + +
684B VAL* 3.0 17.3 + - + +
721B ALA* 4.3 4.7 - - + +
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Residues in contact with ILE 681 (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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550B TRP* 3.9 22.1 - - + -
615B HIS* 5.9 7.2 - - + -
677B LEU 3.1 12.3 + - - +
678B LEU* 3.4 15.7 - - - +
680B HIS* 1.3 75.2 - - - +
682B GLY* 1.3 57.7 + - - +
684B VAL* 3.3 2.8 + - - +
685B GLN* 2.8 32.0 + - - +
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Residues in contact with GLY 682 (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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678B LEU 3.7 4.0 + - - -
679B CYS 3.4 7.2 + - - -
680B HIS 3.2 1.0 - - - -
681B ILE* 1.3 78.8 - - - +
683B VAL* 1.3 56.8 + - - +
685B GLN* 3.7 7.4 - - - +
686B HIS* 3.1 29.1 + - - +
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Residues in contact with VAL 683 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679B CYS 3.5 9.6 + - - +
680B HIS* 3.0 17.0 + - + +
682B GLY* 1.3 73.9 - - - +
684B VAL* 1.3 64.5 + - - +
686B HIS* 3.8 6.8 + - - +
687B ALA* 3.6 16.1 + - - +
721B ALA* 4.3 21.1 - - + +
722B ASN* 5.1 3.4 - - + +
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Residues in contact with VAL 684 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550B TRP* 3.7 28.9 - - + +
551B HIS 4.9 7.0 - - - +
680B HIS* 3.0 23.7 + - + +
681B ILE 3.7 6.1 - - - +
683B VAL* 1.3 74.0 - - - +
685B GLN* 1.3 64.2 + - - +
686B HIS 3.1 1.6 - - - -
687B ALA* 3.0 24.7 + - - +
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Residues in contact with GLN 685 (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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550B TRP* 4.2 11.0 - - + -
618B VAL* 6.4 1.8 - - + -
619B LEU* 5.1 17.2 - - + +
681B ILE 2.8 19.1 + - - +
682B GLY* 3.7 9.2 - - - +
684B VAL* 1.3 75.9 - - - +
686B HIS* 1.3 61.2 + - - +
687B ALA 4.2 4.0 - - - -
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Residues in contact with HIS 686 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682B GLY 3.1 19.0 + - - +
683B VAL* 3.9 8.1 - - - +
684B VAL 3.1 0.2 - - - -
685B GLN* 1.3 73.2 - - - +
687B ALA* 1.3 65.3 + - - +
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Residues in contact with ALA 687 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683B VAL 3.6 9.6 + - - +
684B VAL* 3.0 19.6 + - - +
685B GLN 4.2 4.3 - - - -
686B HIS* 1.3 83.3 - - - +
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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