Contacts of the helix formed by residues 949 - 956 (chain A) in PDB entry 3SQD
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 949 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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907A LYS* 3.3 16.7 - - - +
908A VAL* 2.9 48.1 + - + +
947A LEU* 4.0 3.8 + - + -
948A ARG* 1.3 70.3 - - - +
950A ALA* 1.3 62.5 + - - +
951A GLU* 3.2 10.9 + - - +
952A ALA* 3.1 23.6 + - - +
953A GLU* 2.9 32.1 + - - +
960A LEU* 6.0 0.4 - - - +
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Residues in contact with ALA 950 (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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948A ARG 3.7 5.2 + - - +
949A ASP* 1.3 72.7 + - - +
951A GLU* 1.3 65.5 + - + +
953A GLU* 3.4 9.7 + - - +
954A VAL* 3.1 28.6 + - + +
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Residues in contact with GLU 951 (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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949A ASP* 3.2 8.6 + - - +
950A ALA* 1.3 80.6 - - + +
952A ALA* 1.3 57.7 + - - +
954A VAL* 3.3 6.4 + - - +
955A LEU* 2.8 30.4 + - - +
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Residues in contact with ALA 952 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908A VAL* 3.5 41.7 - - + +
949A ASP* 3.1 19.4 + - - +
951A GLU* 1.3 76.1 - - - +
953A GLU* 1.3 56.3 + - - +
955A LEU* 4.1 9.0 - - + -
956A PHE* 2.8 42.4 + - + -
958A PHE* 3.7 3.3 - - - -
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Residues in contact with GLU 953 (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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908A VAL* 5.5 1.1 - - + -
947A LEU 5.1 1.9 - - - +
948A ARG* 5.1 3.9 - - - +
949A ASP* 2.9 31.3 + - + +
950A ALA* 3.8 9.3 - - - +
951A GLU 3.2 0.4 - - - -
952A ALA* 1.3 74.5 - - + +
954A VAL* 1.3 60.5 + - + +
957A SER* 2.9 23.0 + - - -
958A PHE* 3.0 45.4 + - + +
959A SER* 3.6 8.0 + - - -
960A LEU* 2.8 31.7 + - + +
961A GLU 4.5 0.9 + - - -
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Residues in contact with VAL 954 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
950A ALA* 3.1 16.3 + - + +
951A GLU* 3.7 8.5 - - - +
953A GLU* 1.3 73.6 - - + +
955A LEU* 1.3 72.2 + - - +
957A SER* 3.2 15.1 + - - +
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Residues in contact with LEU 955 (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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951A GLU 2.8 18.0 + - - +
952A ALA* 3.1 9.4 + - - +
954A VAL* 1.3 82.0 - - - +
956A PHE* 1.3 87.0 + - + +
957A SER* 3.7 2.8 + - - -
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Residues in contact with PHE 956 (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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908A VAL* 5.1 3.1 - - + -
910A ARG* 3.3 46.4 - - - -
952A ALA* 2.8 36.2 + - + -
953A GLU 3.8 0.2 - - - -
955A LEU* 1.3 99.1 - - + +
957A SER* 1.3 71.6 + - - +
958A PHE* 3.4 18.3 + + + -
1054A THR* 4.3 16.9 - - + +
1057A LEU* 3.8 18.8 - - + -
1058A THR* 3.8 18.5 - - + +
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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