Contacts of the helix formed by residues 588 - 598 (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 TYR 588 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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442A TYR* 4.0 20.4 - + + -
445A ARG* 3.1 68.9 + - + -
446A ILE* 4.6 4.0 - - + -
449A LEU* 4.1 13.1 - - + +
585A PRO* 3.3 27.8 - - + +
586A GLY 3.0 1.2 + - - -
587A LYS* 1.3 116.1 + - + +
589A SER* 1.3 59.3 + - - +
590A ILE 3.7 0.7 - - - -
591A GLU* 3.8 26.0 - - - +
592A MET* 2.9 29.1 + - - +
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Residues in contact with SER 589 (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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522A LEU* 3.5 29.5 - - - +
579A ILE* 4.1 14.3 + - - +
580A GLU* 4.4 3.6 + - - -
583A PHE* 4.6 0.3 - - - +
585A PRO* 3.8 15.8 - - - +
586A GLY* 2.8 31.8 + - - -
587A LYS 3.3 2.4 - - - -
588A TYR* 1.3 75.0 - - - +
590A ILE* 1.3 68.0 + - - +
592A MET* 2.7 31.7 + - - +
593A SER 3.2 3.3 + - - -
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Residues in contact with ILE 590 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A LEU* 3.8 18.2 - - + -
230A LEU* 3.3 29.7 - - + +
238A TYR* 3.7 18.8 - - + +
522A LEU* 4.0 9.6 - - + -
526A TRP* 4.5 3.6 - - + +
573A ILE* 3.4 59.7 - - + +
579A ILE* 4.5 4.7 - - + -
580A GLU* 4.3 11.2 + - + +
587A LYS 5.1 0.4 + - - -
589A SER* 1.3 84.6 - - - +
591A GLU* 1.3 60.6 + - - +
593A SER* 2.7 24.3 + - - +
594A SER 3.3 2.6 + - - -
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Residues in contact with GLU 591 (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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228A PRO* 4.1 21.4 - - + +
230A LEU* 3.9 11.3 - - + +
236A TYR* 3.7 37.9 + - + -
442A TYR* 2.9 30.9 + - - +
587A LYS 5.2 2.7 + - - +
588A TYR* 3.7 33.5 + - - +
589A SER 3.1 0.8 - - - -
590A ILE* 1.3 75.9 - - - +
592A MET* 1.3 63.7 + - - +
594A SER* 3.0 17.0 + - - -
595A SER* 3.3 2.8 + - - +
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Residues in contact with MET 592 (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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438A ALA* 4.1 17.0 - - - +
439A PHE* 4.4 20.0 - - + -
442A TYR* 3.5 46.2 + - + -
446A ILE* 4.2 4.5 - - + -
519A TYR* 5.9 5.4 - - - -
522A LEU* 4.5 10.3 - - + -
523A VAL* 5.6 3.1 - - + -
585A PRO* 3.5 33.0 - - + -
588A TYR 2.9 10.0 + - - +
589A SER* 2.7 20.4 + - - +
591A GLU* 1.3 71.3 - - - +
593A SER* 1.3 58.8 + - - +
595A SER* 3.2 4.2 + - - -
596A VAL* 3.1 32.9 + - + +
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Residues in contact with SER 593 (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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238A TYR* 2.6 31.8 + - - -
522A LEU* 3.6 30.2 - - - +
523A VAL* 4.8 3.1 - - - -
526A TRP* 4.2 1.9 - - - -
527A LEU* 3.2 11.6 - - - +
589A SER 3.2 4.0 + - - -
590A ILE* 2.7 20.5 + - - +
592A MET* 1.3 76.6 - - - +
594A SER* 1.3 56.6 + - - +
596A VAL* 4.3 7.6 - - - -
597A TYR* 2.9 28.9 + - - +
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Residues in contact with SER 594 (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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230A LEU* 4.1 14.0 - - - +
235A ILE 4.8 1.3 + - - -
236A TYR* 3.7 10.1 - - - -
237A PRO* 2.5 39.4 + - - +
238A TYR* 3.8 11.7 - - - -
590A ILE 3.3 6.1 + - - -
591A GLU* 3.0 15.3 + - - -
593A SER* 1.3 76.7 + - - +
595A SER* 1.3 64.7 + - - +
597A TYR* 3.0 15.6 + - - +
598A LYS* 3.3 11.3 + - - +
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Residues in contact with SER 595 (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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235A ILE 5.6 1.7 + - - -
441A PRO* 6.4 0.7 - - - -
442A TYR* 2.7 35.1 + - - -
591A GLU* 3.3 0.9 + - - +
592A MET 3.2 8.8 + - - -
594A SER* 1.3 77.3 - - - +
596A VAL* 1.3 63.0 + - - +
598A LYS* 3.6 32.9 + - - +
599A ASN* 3.8 8.5 + - - -
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Residues in contact with VAL 596 (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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438A ALA* 5.3 11.0 - - + +
519A TYR* 4.4 17.0 - - + +
523A VAL* 3.5 43.5 - - + -
527A LEU* 4.3 3.1 - - + +
592A MET* 3.1 28.6 + - + +
593A SER* 4.0 4.0 - - - +
595A SER* 1.3 79.3 - - - +
597A TYR* 1.3 61.7 + - - +
598A LYS 3.2 0.7 - - - -
599A ASN* 3.2 26.8 + - + +
600A TRP* 3.7 3.5 + - - +
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Residues in contact with TYR 597 (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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237A PRO* 3.4 28.5 - - + +
238A TYR* 3.5 20.4 - - + -
239A PRO* 3.6 22.5 - - + +
527A LEU* 3.8 21.5 - - + +
532A VAL* 4.3 2.2 - - + -
593A SER 2.9 19.7 + - - +
594A SER* 3.2 9.4 - - - +
596A VAL* 1.3 71.0 - - - +
598A LYS* 1.3 62.2 + - - +
599A ASN 3.1 2.2 - - - -
600A TRP* 3.1 44.5 + + + +
683A HIS* 3.0 39.8 + + - +
685A ASP* 4.7 2.7 - - + -
686A LEU* 3.7 31.4 - - + +
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Residues in contact with LYS 598 (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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234A SER 3.8 21.0 + - - +
235A ILE* 3.9 18.6 + - - +
237A PRO* 3.6 20.0 - - + -
594A SER 3.7 2.7 - - - +
595A SER* 3.6 28.4 + - - +
596A VAL 3.2 0.2 - - - -
597A TYR* 1.3 77.0 - - - +
599A ASN* 1.3 64.6 + - - +
600A TRP 3.8 1.2 + - - +
686A LEU* 4.2 13.6 - - + +
689A LYS* 3.8 20.8 + - - -
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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