Contacts of the helix formed by residues 782 - 789 (chain D) in PDB entry 1ES7
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 GLY 782 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A TYR* 6.0 1.8 - - - -
559C ASN* 3.3 22.1 + - - -
562C ILE* 3.9 8.1 - - - +
780D TYR 3.3 1.0 + - - -
781D GLU* 1.3 73.0 - - - +
783D SER* 1.3 63.0 + - - +
784D ASP* 3.3 12.8 + - - -
785D PHE* 3.2 21.2 + - - +
786D GLN* 3.3 21.2 + - - +
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Residues in contact with SER 783 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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758D HIS* 3.1 38.4 + - - -
778D MET* 3.7 16.6 - - - -
779D LYS 3.5 11.2 - - - -
780D TYR* 2.7 26.2 + - - -
781D GLU 3.2 2.2 + - - -
782D GLY* 1.3 75.2 - - - +
784D ASP* 1.3 63.1 + - - +
787D CYS* 2.8 34.6 + - - +
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Residues in contact with ASP 784 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A TRP* 4.2 18.5 - - + -
91A TYR* 5.4 4.5 + - + -
101A LYS* 4.0 9.4 - - - +
103A TYR* 3.1 33.3 + - - -
780D TYR 5.9 0.2 - - - -
782D GLY* 3.8 10.8 + - - -
783D SER* 1.3 78.8 + - - +
785D PHE* 1.3 77.2 + - - -
787D CYS* 4.7 3.3 - - - +
788D LYS* 3.2 31.0 + - + +
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Residues in contact with PHE 785 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PHE* 6.1 0.9 - + - -
28A TRP* 3.9 31.3 - + - -
31A TRP* 4.0 21.8 - + - -
32A ILE* 4.8 0.9 - - + -
89A MET* 3.8 15.0 - - + -
103A TYR* 3.6 37.0 - + - -
106A MET* 3.7 22.2 - - + -
559C ASN* 4.1 10.3 - - - -
562C ILE* 3.8 15.9 - - + -
563C VAL* 4.1 18.4 - - + -
566C LEU* 3.6 19.6 - - + +
782D GLY* 3.4 16.4 - - - +
783D SER 3.1 0.2 - - - -
784D ASP* 1.3 89.5 + - - +
786D GLN* 1.3 56.6 + - - +
788D LYS* 3.8 1.7 - - - +
789D ASP* 3.1 22.3 + - - -
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Residues in contact with GLN 786 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549C PHE* 3.4 37.2 - - + -
550C PRO* 3.2 12.0 - - + +
551C LEU* 2.7 46.3 + - - +
562C ILE* 3.3 36.0 - - + +
566C LEU* 4.8 0.2 - - - -
778D MET* 3.7 35.2 - - + +
779D LYS 5.4 0.8 + - - +
781D GLU 5.4 1.2 + - - -
782D GLY 3.5 13.6 + - - +
783D SER 3.2 1.2 + - - +
785D PHE* 1.3 75.9 - - - +
787D CYS* 1.3 63.2 + - - +
788D LYS 3.5 0.2 + - - -
789D ASP 3.6 3.6 + - - -
799D ILE* 3.7 9.4 - - - +
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Residues in contact with CYS 787 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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758D HIS* 4.3 12.8 - - - -
778D MET* 3.5 14.1 - - - -
783D SER 2.8 25.2 + - - +
784D ASP* 4.7 3.1 - - - +
786D GLN* 1.3 72.8 - - - +
788D LYS* 1.3 63.6 + - + +
799D ILE* 3.9 17.3 - - - +
800D GLU* 5.7 0.5 - - - -
801D CYS* 2.0 54.4 + - + +
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Residues in contact with LYS 788 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A TRP* 4.6 1.6 - - + +
30A ASP* 4.5 8.6 + - - +
31A TRP* 3.7 60.2 - - + +
92A LEU 5.7 1.5 + - - -
784D ASP* 3.2 23.9 + - + +
785D PHE 3.8 3.1 - - - +
786D GLN 3.2 0.2 - - - -
787D CYS* 1.3 77.3 - - + +
789D ASP* 1.3 78.5 + - - +
790D SER 5.3 0.2 - - - -
791D PRO* 5.6 1.0 - - - +
799D ILE* 5.3 0.2 - - - +
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Residues in contact with ASP 789 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A TRP* 2.9 21.4 + - - -
549C PHE* 3.8 8.9 - - - -
566C LEU* 3.3 11.2 - - - +
785D PHE 3.1 14.7 + - - -
786D GLN 3.6 4.6 + - - +
787D CYS 3.4 0.8 - - - -
788D LYS* 1.3 87.4 - - - +
790D SER* 1.3 81.7 + - - +
791D PRO* 4.0 2.3 - - - +
793D ALA* 5.3 0.2 - - - +
797D ARG* 2.6 60.3 + - - +
798D THR* 5.4 0.2 - - - -
799D ILE* 4.1 20.5 + - + +
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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