Contacts of the helix formed by residues 674 - 688 (chain A) 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 SER 674 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641A TYR* 3.9 24.0 - - - -
645A TYR* 4.3 21.1 - - - -
667A ALA* 4.3 5.5 + - - -
668A LEU* 4.4 3.5 - - - -
671A ASN* 2.3 41.7 + - - +
672A PRO 3.3 0.2 - - - -
673A GLN* 1.3 77.5 - - - +
675A SER* 1.3 67.5 + - - +
676A VAL 3.1 1.0 + - - -
677A LEU* 3.2 12.5 + - - +
678A LEU* 3.4 18.4 - - - +
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Residues in contact with SER 675 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645A TYR* 3.8 29.5 + - - -
673A GLN* 3.3 3.4 + - - -
674A SER* 1.3 78.8 + - - +
676A VAL* 1.3 63.4 + - - +
679A CYS* 2.9 31.7 + - - +
713A PHE* 3.4 25.8 - - - -
717A SER* 3.5 28.7 - - - -
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Residues in contact with VAL 676 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A GLU 4.6 5.8 - - - +
518A LEU 4.6 3.1 - - - +
519A SER* 3.5 33.2 - - - +
521A TYR* 5.6 1.1 - - - +
673A GLN* 3.2 28.1 + - + +
675A SER* 1.3 78.3 - - - +
677A LEU* 1.3 73.8 + - + +
679A CYS* 4.4 1.6 - - - +
680A HIS* 3.1 28.5 + - + +
717A SER* 6.0 0.4 - - - -
720A PHE* 5.6 11.2 - - + -
721A ALA* 5.4 1.4 - - - +
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Residues in contact with LEU 677 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A PHE* 5.4 13.7 - - + +
517A GLU 5.7 2.5 - - - +
519A SER* 5.4 4.5 - - - -
521A TYR* 4.2 14.6 - - + +
551A HIS* 4.0 12.3 - - - +
641A TYR* 4.8 11.4 - - - +
642A ASN* 6.1 1.1 - - - +
673A GLN 5.5 0.4 - - - +
674A SER 3.2 6.7 + - - +
676A VAL* 1.3 85.6 - - + +
678A LEU* 1.3 66.9 + - + +
680A HIS* 3.2 5.4 + - - +
681A ILE* 3.1 24.4 + - - +
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Residues in contact with LEU 678 (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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615A HIS* 3.5 25.0 - - + +
641A TYR* 3.8 28.0 - - + -
642A ASN* 3.4 32.5 - - - +
645A TYR* 3.9 31.0 - - + -
646A GLY* 4.0 7.6 - - - +
649A MET* 6.2 0.7 - - + -
674A SER* 3.4 22.5 + - - +
676A VAL 3.5 0.2 - - - -
677A LEU* 1.3 84.0 - - + +
679A CYS* 1.3 59.6 + - - +
681A ILE* 3.4 21.6 - - - +
682A GLY* 3.8 3.8 + - - -
714A HIS* 5.9 0.6 - - - -
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Residues in contact with CYS 679 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645A TYR* 4.2 1.1 - - - -
675A SER* 2.9 32.8 + - - +
676A VAL* 4.4 0.9 - - - +
678A LEU* 1.3 74.5 - - - +
680A HIS* 1.3 65.5 + - - +
681A ILE 3.1 1.3 - - - -
682A GLY* 3.4 4.2 + - - +
683A VAL* 3.3 23.2 + - - +
714A HIS* 3.4 37.7 - - - -
717A SER* 4.0 7.9 - - - +
718A VAL* 4.1 18.6 - - + -
721A ALA* 3.8 17.8 - - + +
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Residues in contact with HIS 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A TYR* 3.4 38.5 - + - +
551A HIS* 4.1 25.2 + - - +
553A GLN* 6.0 2.2 - - - -
676A VAL* 3.1 25.3 + - + +
677A LEU 3.2 6.3 + - - +
679A CYS* 1.3 74.1 - - - +
681A ILE* 1.3 66.1 + - - +
683A VAL* 3.1 23.0 + - + +
684A VAL* 3.0 21.0 + - + +
721A ALA* 4.3 4.8 - - + +
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Residues in contact with ILE 681 (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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550A TRP* 4.1 25.3 - - + -
551A HIS* 4.3 3.4 - - + -
615A HIS* 4.6 19.3 - - + -
677A LEU 3.1 11.4 + - - +
678A LEU* 3.4 17.0 - - - +
679A CYS 3.1 0.2 - - - -
680A HIS* 1.3 76.0 - - - +
682A GLY* 1.3 62.4 + - - +
684A VAL* 3.0 14.6 + - - +
685A GLN* 3.0 24.0 + - - +
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Residues in contact with GLY 682 (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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678A LEU 3.8 5.1 + - - -
679A CYS* 3.4 7.0 + - - -
680A HIS 3.3 0.4 - - - -
681A ILE* 1.3 78.5 - - - +
683A VAL* 1.3 56.7 + - - +
685A GLN* 3.5 17.5 + - - +
686A HIS* 3.0 31.7 + - - +
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Residues in contact with VAL 683 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679A CYS 3.3 14.7 + - - +
680A HIS* 3.1 24.8 + - + +
682A GLY* 1.3 74.0 - - - +
684A VAL* 1.3 67.6 + - - +
685A GLN 3.2 0.2 + - - -
686A HIS* 3.3 3.9 + - - +
687A ALA* 3.0 29.7 + - + +
718A VAL 5.6 0.2 - - - +
721A ALA* 3.3 40.8 - - + +
722A ASN* 3.8 7.2 - - + +
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Residues in contact with VAL 684 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550A TRP* 3.9 28.0 - - + +
551A HIS* 5.2 4.5 - - - +
553A GLN* 4.5 23.9 + - + +
680A HIS* 3.0 18.8 + - + +
681A ILE 3.5 8.3 - - - +
683A VAL* 1.3 78.8 - - - +
685A GLN* 1.3 62.6 + - - +
687A ALA* 4.1 2.7 - - - +
688A LEU* 3.5 20.6 + - - +
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Residues in contact with GLN 685 (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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550A TRP* 4.9 14.3 - - + -
615A HIS* 3.2 30.5 + - - +
616A GLU* 4.9 1.2 - - - +
618A VAL* 4.8 9.4 - - - +
619A LEU* 3.5 30.5 - - + +
681A ILE* 3.0 21.0 + - - +
682A GLY* 3.5 18.7 + - - +
684A VAL* 1.3 73.2 - - - +
686A HIS* 1.3 58.0 + - - +
687A ALA 3.1 3.8 - - - -
688A LEU* 3.0 29.6 + - - +
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Residues in contact with HIS 686 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682A GLY 3.0 15.8 + - - +
683A VAL* 3.8 3.8 - - - +
685A GLN* 1.3 77.6 - - - +
687A ALA* 1.3 58.4 + - - +
688A LEU 4.9 1.1 - - - -
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Residues in contact with ALA 687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553A GLN* 5.3 7.2 - - - +
683A VAL* 3.0 20.8 + - + +
684A VAL* 4.1 5.4 - - - +
685A GLN 3.1 0.2 - - - -
686A HIS* 1.3 81.2 - - - +
688A LEU* 1.3 58.9 + - - +
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Residues in contact with LEU 688 (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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553A GLN* 6.0 2.5 - - - +
585A LEU 5.8 2.7 - - - +
587A ARG* 5.0 19.1 - - + +
684A VAL 3.5 13.3 + - - +
685A GLN* 3.0 16.0 + - - +
686A HIS 4.9 1.3 - - - -
687A ALA* 1.3 82.0 - - + +
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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