Contacts of the helix formed by residues 742 - 747 (chain A) in PDB entry 3LLT
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 ALA 742 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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736A ASN* 3.3 8.2 + - - +
740A TYR 3.6 1.6 + - - -
741A ARG* 1.3 75.0 - - - +
743A PRO* 1.4 73.0 - - + +
744A GLU* 3.4 26.2 - - - +
745A VAL* 3.0 24.6 + - + +
746A ILE* 3.2 13.0 + - - +
755A SER* 4.0 12.8 - - - +
758A TRP* 3.6 18.2 - - + -
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Residues in contact with PRO 743 (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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741A ARG 3.9 0.4 - - - -
742A ALA* 1.4 83.5 - - - +
744A GLU* 1.3 57.4 + - - +
746A ILE* 3.4 6.2 + - + +
747A LEU* 2.9 37.2 + - + +
758A TRP* 3.6 25.4 - - + +
783A LEU* 4.9 4.9 - - + -
786A MET* 3.6 30.3 - - + -
793A ILE* 6.0 0.9 - - + -
797A MET* 4.3 4.9 - - + -
857A ILE* 3.9 26.7 - - + +
862A ARG* 3.5 24.5 - - - +
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Residues in contact with GLU 744 (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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742A ALA* 3.4 14.8 - - + +
743A PRO* 1.3 71.6 - - - +
745A VAL* 1.3 61.9 + - - +
747A LEU 4.1 0.7 - - - -
748A ASN* 3.2 1.4 + - - -
749A LEU* 2.8 50.4 + - + -
750A GLY 3.5 25.2 + - - +
751A TRP* 4.2 11.2 - - + -
752A ASP 5.5 0.3 + - - -
754A SER* 4.5 0.5 + - - -
755A SER* 3.5 12.5 + - - -
797A MET* 4.4 2.6 - - + +
857A ILE 4.0 2.9 - - - +
859A PRO* 3.7 24.3 - - + +
862A ARG* 2.7 46.5 + - - -
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Residues in contact with VAL 745 (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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733A SER 3.8 18.5 - - - +
734A ILE* 4.1 7.2 - - + +
735A ILE* 3.6 51.8 - - + +
736A ASN* 3.8 4.0 - - - +
741A ARG* 3.9 18.2 - - + -
742A ALA* 3.0 27.1 + - + +
744A GLU* 1.3 76.0 - - + +
746A ILE* 1.3 66.0 + - - +
748A ASN* 3.1 14.4 + - - +
751A TRP* 4.1 18.6 - - + -
755A SER* 4.6 0.7 - - - -
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Residues in contact with ILE 746 (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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734A ILE* 6.3 0.2 - - - -
741A ARG* 3.9 13.7 - - + +
742A ALA 3.2 10.4 + - - +
743A PRO 3.4 5.1 + - - +
745A VAL* 1.3 78.7 - - - +
747A LEU* 1.3 57.2 + - - +
748A ASN* 3.2 6.8 + - - +
779A HIS* 3.6 50.6 + - + +
782A HIS* 3.8 35.2 - - + +
783A LEU* 3.8 28.9 - - + -
786A MET* 3.9 22.0 - - + -
805A ASN 5.4 0.3 - - - +
806A GLY* 4.5 0.9 + - - -
809A TYR* 3.7 15.0 - - + -
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Residues in contact with LEU 747 (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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743A PRO* 2.9 21.5 + - + +
746A ILE* 1.3 73.9 - - - +
748A ASN* 1.3 63.7 + - - +
749A LEU* 3.3 29.4 + - + +
783A LEU* 3.8 34.3 - - + -
793A ILE* 4.3 25.8 - - + -
797A MET* 4.6 13.7 - - + +
798A LEU* 5.0 2.5 - - + -
801A ALA* 4.0 16.8 - - + +
804A THR* 3.0 20.1 + - - -
806A GLY* 3.5 12.8 - - - +
809A TYR* 4.1 14.8 - - + -
810A VAL* 4.6 5.6 - - + -
817A LEU* 5.2 3.4 - - + -
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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