Contacts of the helix formed by residues 967 - 971 (chain A) in PDB entry 3LXL
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 967 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A IZA 3.9 31.7 + - + +
832A ASN* 4.3 10.2 + - - +
871A GLU* 5.4 1.8 - - - -
884A VAL* 5.1 0.4 - - - +
902A MET* 6.2 1.6 - - - -
947A HIS* 3.1 16.6 + - - +
949A ASP* 2.7 33.3 - - - +
954A ASN* 2.9 37.4 + - + +
966A ALA* 1.3 79.6 - - - +
968A PHE* 1.3 58.3 + - - +
969A GLY* 3.2 12.2 + - - +
970A LEU* 4.6 2.8 + - - +
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Residues in contact with PHE 968 (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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871A GLU* 3.7 35.8 + - + +
874A ILE* 4.2 8.9 - - + +
875A LEU* 3.7 21.5 - - + -
878A LEU* 3.6 20.4 - - + -
883A ILE* 3.7 26.2 - - + -
884A VAL* 4.8 0.9 - - + -
940A LEU* 3.7 25.4 - - + -
945A CYS* 4.6 2.0 - - - -
947A HIS* 3.9 6.7 - + - -
965A ILE* 3.6 36.6 - - + -
966A ALA* 3.8 14.1 - - - -
967A ASP* 1.3 73.4 - - - +
969A GLY* 1.3 58.3 + - - +
970A LEU 3.2 3.4 - - - -
971A ALA* 3.1 38.5 + - + +
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Residues in contact with GLY 969 (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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832A ASN* 5.6 8.1 - - - +
855A LYS* 4.7 4.9 - - - -
867A ASP* 4.7 19.5 - - - +
870A ARG* 5.9 0.5 + - - -
871A GLU* 3.4 25.6 + - - -
967A ASP* 3.2 10.3 + - - +
968A PHE* 1.3 77.6 - - - +
970A LEU* 1.3 66.1 + - - +
971A ALA 5.2 0.4 - - - -
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Residues in contact with LEU 970 (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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832A ASN* 3.8 40.4 - - + +
867A ASP* 6.1 0.9 - - - +
870A ARG* 6.2 0.2 - - - -
947A HIS 3.6 11.6 - - - +
948A ARG* 3.0 63.3 + - + +
949A ASP* 3.8 25.4 - - + -
967A ASP* 4.6 4.4 + - - +
968A PHE 3.2 0.6 - - - -
969A GLY* 1.3 81.1 - - - +
971A ALA* 1.3 65.4 + - - +
972A LYS* 3.7 1.3 + - - +
989A SER* 4.0 9.4 - - - +
994A TYR* 6.0 0.4 - - - +
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Residues in contact with ALA 971 (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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870A ARG* 3.7 17.3 + - - -
874A ILE* 3.7 11.2 - - + +
945A CYS* 3.9 17.9 - - - -
946A VAL 3.1 14.4 - - - +
947A HIS* 3.5 9.0 + - - +
968A PHE* 3.1 34.3 + - + +
969A GLY 3.5 0.9 - - - +
970A LEU* 1.3 82.1 - - - +
972A LYS* 1.3 66.3 + - - +
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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