Contacts of the helix formed by residues 755 - 762 (chain A) in PDB entry 2IUK
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 755 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A GLU* 4.0 13.0 + - - +
751A GLU* 2.9 23.2 + - + +
754A LYS* 1.3 76.4 - - + +
756A PRO* 1.3 58.4 - - - +
757A GLN* 3.8 6.2 + - - +
758A LYS* 2.9 41.8 + - + +
759A ALA 3.3 5.2 + - - -
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Residues in contact with PRO 756 (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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310A PHE* 5.2 0.4 - - - -
503A THR* 3.5 32.6 - - + +
506A LEU* 5.6 4.2 - - + +
752A MET 3.1 20.6 - - - +
753A VAL 4.0 5.2 - - - +
754A LYS 3.4 10.8 - - - +
755A ASN* 1.3 82.5 - - - +
757A GLN* 1.3 62.2 + - + +
758A LYS 3.3 0.2 - - - -
759A ALA* 3.4 7.8 + - + +
760A TYR* 3.1 26.2 + - - +
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Residues in contact with GLN 757 (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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308A GLU 4.5 1.1 - - - -
309A SER* 3.3 16.5 - - - -
310A PHE* 2.9 69.9 - - + +
311A GLU 4.7 0.8 - - - +
755A ASN* 3.2 6.6 + - - +
756A PRO* 1.3 79.5 - - + +
758A LYS* 1.3 61.1 + - - +
760A TYR* 4.0 1.6 - - - -
761A LEU* 2.9 30.8 + - - +
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Residues in contact with LYS 758 (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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306A GLU* 3.4 32.1 + - - +
307A PHE 2.9 25.0 + - - +
308A GLU* 3.6 31.2 - - - +
751A GLU* 5.6 1.1 - - + +
755A ASN* 2.9 33.3 + - + +
757A GLN* 1.3 74.3 - - - +
759A ALA* 1.3 57.6 + - - +
760A TYR 2.9 1.7 + - - -
761A LEU* 3.2 2.1 + - + -
762A ARG* 2.9 69.2 + - + +
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Residues in contact with ALA 759 (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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507A LEU* 3.5 4.7 - - + +
739A ARG* 2.8 17.6 + - - +
751A GLU 4.4 0.6 + - - +
752A MET* 3.8 39.9 - - + -
755A ASN 3.3 3.7 + - - +
756A PRO 3.4 10.3 + - - +
758A LYS* 1.3 78.4 - - - +
760A TYR* 1.3 48.7 + - - +
762A ARG* 3.8 26.1 - - - +
763A THR* 2.7 27.2 + - - -
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Residues in contact with TYR 760 (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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310A PHE* 3.5 31.4 - + + -
364A VAL* 4.4 5.5 + - + -
506A LEU* 3.7 47.9 - - + +
507A LEU* 3.8 17.7 - - + -
510A ALA* 3.8 20.7 - - + +
731A LEU* 2.8 48.1 + - + -
734A PRO* 4.4 4.9 - - - +
756A PRO 3.1 15.4 + - - +
757A GLN 4.1 0.7 - - - +
758A LYS 3.1 0.4 - - - -
759A ALA* 1.3 72.1 - - - +
761A LEU* 1.3 58.4 + - - +
762A ARG 3.1 4.5 - - - -
763A THR* 2.9 20.4 + - - -
764A ILE* 3.0 33.8 + - + +
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Residues in contact with LEU 761 (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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306A GLU* 3.6 7.6 - - - +
307A PHE* 3.7 31.9 - - + +
308A GLU 3.7 3.1 - - - -
309A SER 3.3 38.4 - - - +
310A PHE* 4.0 6.5 - - + -
313A VAL* 3.6 27.8 - - + -
730A ILE* 5.2 0.2 - - + -
731A LEU* 3.8 17.0 - - + -
738A ARG* 2.8 22.7 + - - -
757A GLN 2.9 21.5 + - - +
758A LYS* 3.8 3.6 - - - +
760A TYR* 1.3 80.1 - - - +
762A ARG* 1.4 50.9 + - - +
763A THR 3.3 0.2 - - - -
764A ILE* 3.8 20.1 + - + +
765A THR 4.6 3.8 - - - +
766A PRO* 5.0 0.5 - - - +
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Residues in contact with ARG 762 (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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306A GLU* 4.7 0.2 - - - -
738A ARG* 3.0 28.7 + - - +
739A ARG* 3.4 33.9 - - + +
742A PRO* 4.7 0.2 - - - +
748A GLU* 2.8 43.1 + - - +
751A GLU* 3.5 28.1 - - - +
758A LYS* 2.9 47.1 + - - +
759A ALA* 3.8 29.1 - - - +
760A TYR 3.1 0.2 - - - -
761A LEU* 1.4 73.2 - - - +
763A THR* 1.4 53.6 + - - +
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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