Contacts of the helix formed by residues 703 - 714 (chain A) in PDB entry 2H5G
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 ASP 703 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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591A GLU* 4.0 21.6 - - + +
701A THR* 3.2 16.8 + - - +
702A GLU* 1.3 77.5 - - - +
704A GLU* 1.3 63.1 + - - +
705A ASN* 3.5 18.6 + - - +
706A THR* 2.7 29.8 + - - +
707A ALA* 3.1 18.8 + - - +
721A TRP* 4.6 0.2 - - - -
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Residues in contact with GLU 704 (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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702A GLU 3.3 5.4 + - - +
703A ASP* 1.3 70.2 + - - +
705A ASN* 1.3 63.0 + - - +
707A ALA* 3.4 0.9 + - - +
708A GLU* 2.9 46.9 + - + +
721A TRP* 3.6 32.0 - - + -
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Residues in contact with ASN 705 (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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703A ASP* 3.4 14.4 + - - +
704A GLU* 1.3 80.4 - - - +
706A THR* 1.3 58.2 + - - +
708A GLU* 3.5 4.6 + - - +
709A PHE* 3.0 28.8 + - - +
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Residues in contact with THR 706 (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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589A ASP* 3.8 19.8 + - - +
681A VAL* 3.4 33.8 - - + +
699A ILE* 3.9 13.2 - - + -
701A THR* 4.6 0.7 - - - +
703A ASP* 2.7 35.4 + - - +
704A GLU 3.3 0.2 - - - -
705A ASN* 1.3 75.5 - - - +
707A ALA* 1.3 65.0 + - - +
709A PHE* 3.2 9.7 + - - +
710A PHE* 3.0 22.3 + - - +
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Residues in contact with ALA 707 (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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699A ILE* 4.2 7.6 - - - -
701A THR* 3.6 7.9 - - + +
703A ASP 3.1 9.9 + - - +
704A GLU 3.6 8.5 - - - +
706A THR* 1.3 77.1 - - - +
708A GLU* 1.3 55.3 + - - +
710A PHE* 3.4 4.0 + - - +
711A LEU* 2.9 34.5 + - - +
721A TRP* 3.3 51.8 - - + +
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Residues in contact with GLU 708 (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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704A GLU* 2.9 34.0 + - + +
705A ASN* 4.0 5.4 - - - +
707A ALA* 1.3 72.4 - - + +
709A PHE* 1.3 59.1 + - - +
711A LEU* 3.8 25.1 - - - +
712A GLN* 3.0 31.7 + - - +
721A TRP* 3.9 17.7 - - - -
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Residues in contact with PHE 709 (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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681A VAL* 4.3 17.9 - - + -
682A GLN* 3.9 21.8 - - + -
685A ILE* 3.9 22.0 - - + -
705A ASN 3.0 14.6 + - - +
706A THR* 3.2 11.9 - - - +
708A GLU* 1.3 75.9 - - - +
710A PHE* 1.3 57.3 + - - +
712A GLN* 3.3 3.0 + - - -
713A HIS* 2.6 67.8 + + - +
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Residues in contact with PHE 710 (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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587A TYR* 3.8 21.3 - + + -
681A VAL* 4.0 18.4 - - + -
684A ALA* 4.5 5.2 - - + -
685A ILE* 4.1 16.6 - - + -
688A ILE* 3.6 27.8 - - + -
697A ASP 4.2 1.3 - - - -
698A VAL* 3.6 23.1 - - - -
699A ILE* 3.4 41.5 - - + -
706A THR 3.0 12.4 + - - +
707A ALA 3.4 8.7 - - - +
709A PHE* 1.3 71.8 - - - +
711A LEU* 1.3 61.8 + - + +
714A VAL* 3.0 43.8 + - + +
719A VAL* 3.7 22.9 - - + -
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Residues in contact with LEU 711 (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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699A ILE* 4.2 0.9 - - + -
707A ALA 2.9 21.9 + - - +
708A GLU* 3.8 31.4 - - - +
710A PHE* 1.3 80.8 - - + +
712A GLN* 1.3 61.0 + - - +
714A VAL 3.9 10.9 - - - +
719A VAL* 3.8 30.9 - - + +
720A PHE 3.6 31.0 - - - +
721A TRP* 4.0 21.1 - - + +
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Residues in contact with GLN 712 (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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708A GLU 3.0 17.4 + - - +
709A PHE* 3.5 6.3 - - - +
711A LEU* 1.3 79.7 - - - +
713A HIS* 1.3 77.9 + - + +
714A VAL 4.4 2.4 - - - +
715A ASP* 4.7 3.6 - - - +
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Residues in contact with HIS 713 (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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682A GLN* 5.8 2.5 - - - +
685A ILE* 4.0 20.5 - - + +
689A HIS* 2.9 22.2 + - - -
709A PHE* 2.6 67.7 + + - +
712A GLN* 1.3 95.8 - - + +
714A VAL* 1.3 63.8 + - - +
715A ASP* 3.3 8.0 - - - +
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Residues in contact with VAL 714 (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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685A ILE* 3.8 25.1 - - + -
688A ILE* 4.0 19.3 - - + -
689A HIS* 3.5 5.2 - - + -
697A ASP* 4.1 5.8 - - + -
710A PHE* 3.0 41.6 + - + +
711A LEU 3.9 6.9 - - - +
712A GLN 4.4 2.4 - - - +
713A HIS* 1.3 75.5 - - - +
715A ASP* 1.3 60.7 + - - +
716A SER* 3.4 28.1 + - - +
719A VAL* 3.6 30.6 - - + +
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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