Contacts of the helix formed by residues 734 - 744 (chain A) in PDB entry 3L2P
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 ASN 734 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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628A CYS* 4.1 4.7 - - - -
629A TYR* 3.0 27.6 - - + +
631A PRO* 3.7 19.2 - - + +
732A ALA 4.5 2.6 - - - +
733A THR* 1.3 76.7 - - - +
735A LEU* 1.3 66.4 + - - +
736A PRO* 3.4 28.7 - - - +
737A GLN* 2.8 40.9 + - - +
738A LEU* 3.1 10.5 + - - -
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Residues in contact with LEU 735 (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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628A CYS* 3.8 10.5 - - - -
629A TYR 3.3 6.1 + - - -
630A ASP* 3.3 36.1 - - + +
637A CYS* 4.9 8.5 - - - -
710A ALA* 4.9 10.3 - - + -
711A ASP* 4.3 32.5 - - + +
713A ILE* 5.3 3.1 - - + -
734A ASN* 1.3 74.6 - - - +
736A PRO* 1.4 68.8 - - + +
738A LEU* 3.1 5.1 + - - +
739A LYS* 2.8 39.2 + - + +
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Residues in contact with PRO 736 (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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630A ASP* 4.2 2.0 - - - +
631A PRO* 4.1 12.8 - - + -
734A ASN* 3.4 22.7 - - - +
735A LEU* 1.4 96.2 - - + +
737A GLN* 1.3 60.0 + - - +
739A LYS* 3.3 11.0 + - + +
740A GLU* 3.0 22.9 + - - +
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Residues in contact with GLN 737 (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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731A SER 5.0 3.6 + - - +
732A ALA 3.7 6.2 - - - +
733A THR* 3.5 26.6 + - + +
734A ASN* 2.8 30.5 + - - +
736A PRO* 1.3 79.6 - - - +
738A LEU* 1.3 56.2 + - - +
740A GLU* 3.2 9.4 + - - +
741A LEU* 3.0 31.0 + - + +
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Residues in contact with LEU 738 (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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603A ALA* 4.3 19.5 - - + -
605A LEU* 5.6 3.4 - - + -
628A CYS* 5.5 5.2 - - + -
639A VAL* 3.8 29.2 - - + -
710A ALA* 4.9 3.8 - - + -
713A ILE* 3.5 31.6 - - + -
715A ILE* 5.8 3.8 - - + -
733A THR* 3.6 11.4 - - + +
734A ASN 3.1 12.0 + - - +
735A LEU* 3.6 7.9 - - - +
737A GLN* 1.3 70.7 - - - +
739A LYS* 1.3 67.7 + - - +
740A GLU 3.0 1.8 - - - -
741A LEU* 2.9 36.2 + - + +
742A TYR* 3.0 16.2 + - + +
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Residues in contact with LYS 739 (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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711A ASP* 4.2 25.3 - - + +
713A ILE* 4.2 14.9 - - + +
735A LEU* 2.8 20.4 + - + +
736A PRO* 3.3 16.6 - - + +
738A LEU* 1.3 75.6 - - - +
740A GLU* 1.3 62.0 + - - +
742A TYR* 3.8 22.9 - - - +
743A GLN* 3.7 23.1 + - - +
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Residues in contact with GLU 740 (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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736A PRO 3.0 11.8 + - - +
737A GLN* 3.2 11.7 - - - +
738A LEU 3.0 0.4 - - - -
739A LYS* 1.3 75.0 - - - +
741A LEU* 1.3 75.5 + - - +
743A GLN* 2.9 17.9 + - + +
744A LEU* 3.3 41.9 + - + +
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Residues in contact with LEU 741 (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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602A THR 4.0 20.6 - - - +
603A ALA* 5.0 0.7 - - + -
733A THR* 4.5 13.7 - - + +
737A GLN* 3.0 15.4 + - + +
738A LEU* 2.9 36.1 + - + +
740A GLU* 1.3 85.9 - - - +
742A TYR* 1.3 65.6 + - - +
743A GLN 3.3 0.2 + - - -
744A LEU* 3.4 20.0 + - + +
745A SER* 3.8 6.9 + - - -
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Residues in contact with TYR 742 (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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702A PHE* 3.8 44.8 - - + +
703A SER 4.2 1.8 - - - -
704A LYS* 3.5 30.8 + - + +
713A ILE* 3.8 23.6 - - + -
738A LEU* 3.0 12.5 + - + +
739A LYS* 3.8 24.0 - - - +
741A LEU* 1.3 78.4 - - - +
743A GLN* 1.3 77.3 + - + +
745A SER* 3.0 32.1 + - - +
746A LYS* 5.8 5.0 + - + +
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Residues in contact with GLN 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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739A LYS* 3.7 17.5 + - - +
740A GLU* 2.9 12.3 + - + +
742A TYR* 1.3 91.2 - - + +
744A LEU* 1.3 64.9 - - + +
745A SER 3.0 6.4 + - - -
746A LYS* 3.5 43.6 + - - +
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Residues in contact with LEU 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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740A GLU* 3.3 41.5 + - + +
741A LEU* 3.6 17.0 - - + +
742A TYR 3.3 0.6 - - - -
743A GLN* 1.3 77.2 - - + +
745A SER* 1.3 57.9 + - - +
746A LYS 3.3 7.2 + - - +
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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