Contacts of the helix formed by residues 990 - 994 (chain A) in PDB entry 3LXK
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 PRO 990 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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953A ARG* 4.0 25.5 + - - +
988A GLN 4.6 1.1 - - - +
989A SER* 1.3 89.8 - - - +
991A ILE* 1.3 59.5 + - + +
992A PHE* 3.0 18.6 + - + -
993A TRP* 3.7 31.9 + - + +
994A TYR* 4.2 5.0 - - - -
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Residues in contact with ILE 991 (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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987A GLY 5.9 1.3 - - - +
989A SER 4.1 8.1 - - - +
990A PRO* 1.3 71.4 - - - +
992A PHE* 1.3 81.8 + - + +
993A TRP 3.3 0.9 - - - -
994A TYR* 3.3 42.8 + - + +
999A LEU* 4.0 10.3 - - + +
1038A MET* 5.3 1.1 - - - -
1046A ALA* 4.1 15.5 - - + +
1047A LEU* 4.0 36.3 - - + +
1050A LEU* 3.5 31.4 - - + +
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Residues in contact with PHE 992 (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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990A PRO* 3.0 8.7 + - + -
991A ILE* 1.3 103.3 - - + +
993A TRP* 1.3 76.6 + + + +
994A TYR 5.1 0.7 - - - -
1011A TRP* 5.1 1.9 + - - -
1015A VAL* 3.9 14.6 - - - +
1030A PRO* 4.0 15.3 - - + -
1031A SER* 3.3 30.5 - - - -
1034A PHE* 3.7 38.9 - + + -
1035A LEU* 3.8 25.4 - - + -
1038A MET* 3.5 25.4 - - + -
1050A LEU* 4.1 10.5 - - + -
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Residues in contact with TRP 993 (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 6.4 0.4 - - - -
950A LEU 3.4 23.1 - - - +
951A ALA* 3.6 5.2 - - + +
953A ARG* 3.7 31.9 - - - +
990A PRO* 3.7 30.0 + - + +
991A ILE 3.3 0.6 - - - -
992A PHE* 1.3 97.4 - + + +
994A TYR* 1.3 64.0 + - + +
1011A TRP* 3.4 11.1 - - - -
1012A SER* 2.8 33.4 + - - +
1015A VAL* 3.3 29.9 - - + +
1019A GLU* 3.0 41.9 + - - -
1029A SER* 6.3 0.2 - - - -
1030A PRO* 4.0 18.8 - - + -
1031A SER* 5.2 3.8 - - - -
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Residues in contact with TYR 994 (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* 5.0 9.2 - - + -
987A GLY* 3.3 25.6 - - - -
988A GLN 3.5 0.2 + - - -
989A SER* 3.2 54.2 + - - -
990A PRO 4.2 1.8 - - - -
991A ILE* 3.3 34.1 + - + +
992A PHE 5.1 1.0 - - - +
993A TRP* 1.3 79.7 - - + +
995A ALA* 1.3 64.1 + - - +
996A PRO 3.8 0.3 - - - -
998A SER* 4.3 5.8 - - - -
999A LEU* 3.6 35.2 - - + +
1004A PHE* 3.8 37.0 - + - -
1011A TRP* 3.3 13.1 + - - -
1012A SER* 4.9 0.4 - - - -
1047A LEU* 6.1 0.9 - - + -
1050A LEU* 5.8 0.2 - - - +
1054A LEU* 4.5 2.8 - - - +
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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