Contacts of the helix formed by residues 984 - 993 (chain C) in PDB entry 1XD2
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 984 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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761C VAL* 4.6 14.8 - - + +
763C TRP* 3.0 29.7 - - + -
768C PRO* 5.4 0.9 - - - +
787C GLN* 3.0 23.3 + - - +
983C VAL* 1.3 73.7 - - - +
985C SER* 1.3 66.3 + - - +
986C ASP* 3.1 37.4 + - - +
987C ILE* 3.2 29.8 - - + +
988C LYS* 3.0 18.7 + - - +
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Residues in contact with SER 985 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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983C VAL* 3.8 9.9 + - - +
984C GLU* 1.3 73.1 + - - +
986C ASP* 1.3 60.6 + - - +
988C LYS* 3.2 11.1 + - - +
989C ARG* 2.9 54.2 + - - +
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Residues in contact with ASP 986 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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769C GLY* 3.8 24.6 + - - -
771C ILE* 3.4 32.7 - - + +
774C PHE* 3.6 13.4 - - + -
984C GLU* 3.1 16.0 + - - +
985C SER* 1.3 75.3 - - - +
987C ILE* 1.3 58.2 + - - +
989C ARG* 3.2 25.7 + - - +
990C PHE* 3.0 27.2 + - - +
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Residues in contact with ILE 987 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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762C GLU 5.4 0.4 - - - +
763C TRP* 3.9 17.0 - - + -
774C PHE* 3.8 19.7 - - + -
779C LEU* 3.9 22.2 - - + -
783C GLU* 3.7 30.3 - - + +
787C GLN* 3.4 23.6 - - + -
984C GLU* 3.1 28.3 + - + +
986C ASP* 1.3 74.1 - - - +
988C LYS* 1.3 67.5 + - - +
990C PHE* 3.3 3.6 + - - +
991C PHE* 3.3 40.1 + - + -
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Residues in contact with LYS 988 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787C GLN* 4.7 13.0 + - - +
791C LEU* 3.9 24.5 - - + +
794C ASP* 4.3 15.5 + - - +
983C VAL* 4.4 24.2 - - + -
984C GLU 3.0 12.4 + - - +
985C SER* 3.4 12.3 - - - +
987C ILE* 1.3 75.9 - - - +
989C ARG* 1.3 59.5 + - - +
991C PHE* 3.2 8.1 + - - +
992C GLU* 3.0 59.1 + - - +
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Residues in contact with ARG 989 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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771C ILE* 6.2 1.9 - - + +
985C SER* 2.9 35.5 + - - +
986C ASP* 3.2 28.9 + - - +
988C LYS* 1.3 76.6 - - - +
990C PHE* 1.3 65.6 + - - +
992C GLU* 3.6 16.1 - - - +
993C ASN* 3.0 47.3 + - - +
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Residues in contact with PHE 990 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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771C ILE* 5.0 6.3 - - + -
774C PHE* 3.6 48.0 - + + -
775C ASP* 4.2 15.9 - - - -
779C LEU* 4.6 5.6 - - + -
834C TRP* 4.1 12.8 - + - -
986C ASP 3.0 14.6 + - - +
987C ILE* 3.3 8.9 + - - +
989C ARG* 1.3 77.2 - - - +
991C PHE* 1.3 96.7 + + - +
993C ASN* 3.7 4.7 + - - +
994C LEU* 3.4 40.7 + - + +
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Residues in contact with PHE 991 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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779C LEU* 4.4 4.3 - - + -
784C ILE* 3.5 41.3 - - + -
787C GLN* 4.8 4.3 - - + -
788C LEU* 3.7 36.3 - - + -
791C LEU* 3.9 12.1 - - + +
827C HIS* 4.8 6.9 + - - -
831C LEU* 4.5 0.4 - - + -
834C TRP* 3.9 24.7 - + - -
987C ILE* 3.3 36.9 + - + +
988C LYS* 3.2 7.6 + - - +
989C ARG 3.1 0.2 - - - -
990C PHE* 1.3 105.1 - + - +
992C GLU* 1.3 61.5 + - - +
994C LEU* 3.5 32.0 - - + +
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Residues in contact with GLU 992 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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791C LEU* 3.8 20.5 - - + +
827C HIS* 6.2 0.2 - - - -
988C LYS* 3.0 46.8 + - - +
989C ARG* 3.1 27.3 + - - +
991C PHE* 1.3 77.3 - - - +
993C ASN* 1.3 66.7 + - - +
994C LEU 3.3 6.2 + - - +
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Residues in contact with ASN 993 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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989C ARG* 3.0 33.7 + - - +
990C PHE* 3.9 4.5 - - - +
992C GLU* 1.3 85.6 - - - +
994C LEU* 1.3 64.2 + - - +
995C ASN* 3.3 8.0 + - - +
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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