Contacts of the helix formed by residues 736 - 749 (chain A) in PDB entry 5HLB
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 736 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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699A THR* 3.9 12.8 - - + -
700A GLY 3.6 21.5 - - - +
701A THR* 3.1 7.5 + - - -
708A THR* 3.9 9.9 - - - -
709A TRP 3.1 27.8 - - - +
710A PHE* 4.5 1.1 - - + -
734A TYR 3.3 0.6 - - - -
735A GLY* 1.4 78.7 - - - +
737A SER* 1.4 51.3 + - - +
738A GLY 3.2 3.4 + - - -
739A ALA 3.3 1.4 + - - -
740A MET* 2.6 42.5 + - + +
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Residues in contact with SER 737 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A LEU* 4.6 0.9 - - - +
465A ARG* 4.7 12.2 + - - -
685A GLN* 5.5 4.3 + - - -
708A THR* 4.5 1.2 - - - +
733A LEU* 3.8 19.7 - - - +
734A TYR 3.2 23.0 + - - -
735A GLY 3.1 5.5 + - - -
736A ALA* 1.4 74.8 - - - +
738A GLY* 1.3 61.1 + - - +
740A MET* 4.1 4.7 - - - -
741A SER* 3.1 27.2 + - - -
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Residues in contact with GLY 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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461A LEU* 3.9 13.2 - - - +
708A THR* 3.7 10.4 + - - -
723A VAL* 3.8 13.2 - - - -
733A LEU* 3.6 20.7 - - - +
736A ALA 3.3 0.8 - - - -
737A SER* 1.3 81.5 - - - +
739A ALA* 1.3 61.3 + - - +
741A SER* 3.2 3.3 + - - -
742A ILE* 3.2 24.1 + - - +
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Residues in contact with ALA 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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708A THR* 3.2 33.1 + - - +
709A TRP 3.7 9.0 - - - -
710A PHE* 3.9 2.4 - - - +
721A THR* 3.3 40.7 - - + +
723A VAL* 3.7 11.8 - - - +
736A ALA 3.3 2.2 + - - +
738A GLY* 1.3 73.4 - - - +
740A MET* 1.3 57.2 + - - +
743A TYR* 3.1 25.3 + - - +
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Residues in contact with MET 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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682A THR 3.6 21.3 - - - +
683A GLY* 3.7 13.7 - - - -
685A GLN* 4.7 13.0 - - + +
686A LEU* 3.5 42.7 - - + +
699A THR* 3.7 11.7 - - + -
710A PHE* 3.7 19.2 - - + +
735A GLY 3.2 26.7 - - - +
736A ALA 2.6 24.2 + - - +
737A SER* 4.4 3.6 - - - +
739A ALA* 1.3 73.4 - - - +
741A SER* 1.4 56.7 + - - +
743A TYR* 3.5 7.1 + - - +
744A GLN* 3.0 26.4 + - - +
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Residues in contact with SER 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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461A LEU* 4.0 20.0 - - - +
737A SER 3.1 22.1 + - - -
738A GLY 3.2 6.1 + - - -
740A MET* 1.4 73.1 - - - +
742A ILE* 1.3 64.4 + - - +
744A GLN* 3.6 16.7 - - - +
745A ARG* 3.2 31.3 + - - +
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Residues in contact with ILE 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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453A ALA* 3.6 16.2 - - + +
454A ALA* 4.6 1.6 - - - +
457A GLY* 3.7 37.0 - - - -
458A ILE* 4.0 10.5 - - + +
461A LEU* 3.7 15.5 - - + -
472A THR* 4.2 6.7 - - - +
474A ILE* 3.8 28.5 - - + -
721A THR* 3.8 17.5 - - + -
723A VAL* 3.7 17.0 - - + -
738A GLY 3.2 14.0 + - - +
739A ALA 3.8 0.4 - - - +
740A MET 3.3 0.2 - - - -
741A SER* 1.3 74.8 - - - +
743A TYR* 1.4 60.0 + - - +
745A ARG* 3.3 8.4 + - - +
746A TYR* 3.0 23.1 + - - +
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Residues in contact with TYR 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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686A LEU* 3.6 27.8 - - + -
695A LEU* 4.0 14.4 - - + +
710A PHE* 3.6 29.4 - + + -
712A GLY* 3.7 23.2 + - - -
713A ILE 4.1 0.9 + - - -
714A ASP* 4.7 5.6 + - - -
719A THR* 3.8 37.2 - - + -
721A THR* 4.0 11.1 - - - +
739A ALA 3.1 18.3 + - - +
740A MET* 3.5 5.8 - - - +
742A ILE* 1.4 73.9 - - - +
744A GLN* 1.4 53.4 + - - +
746A TYR* 3.1 13.0 + + - +
747A LEU* 2.9 69.8 + - + +
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Residues in contact with GLN 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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686A LEU* 4.7 9.9 - - + -
689A LYS* 4.2 33.2 + - + +
690A TYR* 3.2 27.3 + - + -
740A MET 3.0 17.7 + - - +
741A SER* 3.6 20.5 - - - +
743A TYR* 1.4 76.1 - - - +
745A ARG* 1.3 66.1 + - - +
747A LEU* 3.5 10.2 + - - +
748A ALA* 3.1 30.1 + - - +
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Residues in contact with ARG 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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453A ALA* 3.8 17.9 - - + +
456A GLU* 3.6 29.1 + - - +
457A GLY* 3.3 29.3 - - - -
460A ALA* 3.6 25.3 - - - +
464A GLN* 5.7 0.2 + - - -
741A SER* 3.2 18.7 + - - +
742A ILE* 3.5 9.2 - - - +
743A TYR 3.2 0.4 - - - -
744A GLN* 1.3 86.3 + - - +
746A TYR* 1.4 58.2 + - - +
748A ALA* 3.2 6.8 + - - +
749A ASN* 2.9 41.2 + - - +
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Residues in contact with TYR 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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446A ALA* 3.4 33.8 - - - +
449A ALA* 3.8 10.1 - - + -
450A ALA* 3.5 28.0 - - + -
453A ALA* 3.7 11.2 - - + +
474A ILE* 5.1 7.2 - - + -
476A VAL* 3.4 32.0 - - + +
714A ASP* 5.5 1.3 - - - -
717A THR* 5.0 5.4 + - - +
719A THR* 3.8 22.4 - - + -
742A ILE 3.0 13.2 + - - +
743A TYR* 3.1 30.9 + + + +
745A ARG* 1.4 74.3 - - - +
747A LEU* 1.4 64.6 + - + +
749A ASN* 3.4 6.8 + - - +
750A GLN* 3.3 46.8 + - - +
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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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686A LEU* 3.7 19.3 - - + -
690A TYR* 3.9 28.9 - - + -
695A LEU* 4.0 10.3 - - + -
714A ASP* 4.8 4.5 - - - +
743A TYR* 2.9 65.1 + - + +
744A GLN* 3.7 5.6 - - - +
746A TYR* 1.4 81.2 - - + +
748A ALA* 1.3 55.4 - - - +
750A GLN* 3.0 27.3 + - - +
752A PRO* 3.5 38.6 - - + +
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Residues in contact with ALA 748 (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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690A TYR* 3.3 19.9 + - - +
744A GLN* 3.1 23.2 + - - +
745A ARG* 3.2 7.8 + - - +
747A LEU* 1.3 74.8 - - - +
749A ASN* 1.4 64.0 + - - +
750A GLN 3.4 3.2 + - - +
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Residues in contact with ASN 749 (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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126A LYS* 3.5 17.3 + - - -
449A ALA* 3.2 39.7 + - + +
452A LYS* 2.9 42.5 + - - +
453A ALA* 3.5 15.8 - - - +
456A GLU* 4.9 1.7 + - - +
745A ARG* 2.9 25.9 + - - +
746A TYR 3.8 1.3 - - - +
747A LEU 3.3 1.0 - - - -
748A ALA* 1.4 80.6 - - - +
750A GLN* 1.4 59.3 + - - +
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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