Contacts of the helix formed by residues 562 - 573 (chain A) in PDB entry 3IW4
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 SER 562 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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437A GLU* 2.8 40.8 + - - -
560A SER 3.7 4.2 + - - -
561A LEU* 1.3 75.5 - - - +
563A LYS* 1.3 64.4 - - - +
564A GLU* 3.4 10.9 + - - -
565A ALA* 2.9 17.9 + - - +
566A VAL* 3.1 8.5 + - - +
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Residues in contact with LYS 563 (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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561A LEU 3.5 1.4 + - - -
562A SER* 1.3 71.0 - - - +
564A GLU* 1.3 81.4 + - - +
566A VAL* 3.3 8.4 + - - +
567A SER* 3.1 27.1 + - - -
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Residues in contact with GLU 564 (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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437A GLU* 4.4 1.7 - - - +
562A SER* 3.2 11.3 + - - +
563A LYS* 1.3 102.5 + - - +
565A ALA* 1.3 66.3 + - - +
567A SER* 4.2 5.8 - - - -
568A ILE 3.1 19.2 + - - -
594A HIS* 3.5 3.2 - - - -
595A ALA* 3.3 28.4 - - + +
596A PHE* 3.4 24.0 - - + +
598A ARG* 2.8 38.2 + - - +
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Residues in contact with ALA 565 (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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437A GLU* 3.8 11.4 - - - +
532A LEU* 4.3 12.8 - - + -
561A LEU* 3.9 23.6 - - + -
562A SER* 2.9 21.5 + - - +
564A GLU* 1.3 77.5 - - - +
566A VAL* 1.3 62.4 + - - +
568A ILE* 3.5 1.6 - - - +
569A CYS* 3.2 30.0 + - - -
596A PHE* 3.5 18.7 - - + -
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Residues in contact with VAL 566 (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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557A TYR* 3.6 33.9 - - + -
558A PRO 5.1 0.9 - - - +
561A LEU* 3.6 33.2 - - + +
562A SER 3.1 15.1 + - - +
563A LYS* 3.8 7.4 - - - +
565A ALA* 1.3 76.7 - - - +
567A SER* 1.3 61.1 + - - +
569A CYS* 3.7 1.0 + - - +
570A LYS* 3.1 40.3 + - - +
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Residues in contact with SER 567 (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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563A LYS 3.1 16.5 + - - -
564A GLU* 3.6 2.7 - - - -
565A ALA 3.2 0.4 - - - -
566A VAL* 1.3 76.5 - - - +
568A ILE* 1.3 54.3 + - - +
570A LYS* 3.0 6.2 + - - +
571A GLY* 2.7 33.3 + - - -
594A HIS* 2.7 30.8 + - - -
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Residues in contact with ILE 568 (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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524A TYR* 5.0 1.3 - - + -
528A LEU* 3.6 23.1 - - + -
564A GLU 3.1 4.2 + - - +
565A ALA 3.5 11.0 - - - +
567A SER* 1.3 78.4 - - - +
569A CYS* 1.3 57.5 + - - +
571A GLY 4.2 0.7 - - - +
572A LEU* 2.7 60.4 + - + +
581A LEU* 3.6 17.3 - - + -
591A VAL* 4.8 4.5 - - + -
594A HIS* 3.2 24.4 - - + +
596A PHE* 3.7 30.5 - - + -
597A PHE* 3.7 30.1 - - + -
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Residues in contact with CYS 569 (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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525A GLY* 4.8 1.3 - - - -
528A LEU* 4.5 10.8 - - - -
529A TYR* 4.4 19.7 - - - -
532A LEU* 4.1 22.4 - - - -
557A TYR* 3.1 36.9 + - + +
561A LEU* 5.7 1.8 - - - -
565A ALA 3.2 24.1 + - - +
566A VAL 3.8 0.7 - - - +
567A SER 3.1 0.8 - - - -
568A ILE* 1.3 76.4 - - - +
570A LYS* 1.3 59.0 + - - +
572A LEU* 4.8 3.6 - - - -
573A MET* 2.7 42.5 + - + +
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Residues in contact with LYS 570 (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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554A ASN* 5.9 2.8 - - - +
555A VAL 5.1 2.6 + - - -
557A TYR* 3.4 35.5 - - + +
566A VAL* 3.1 29.6 + - - +
567A SER* 3.0 6.7 + - - +
569A CYS* 1.3 72.3 - - - +
571A GLY* 1.3 58.8 + - - +
573A MET 3.7 3.1 - - - +
574A THR* 2.7 36.1 + - - -
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Residues in contact with GLY 571 (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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567A SER 2.7 14.1 + - - -
568A ILE 3.5 4.0 - - - -
570A LYS* 1.3 81.4 - - - +
572A LEU* 1.3 58.5 + - - +
574A THR* 3.1 12.4 + - - -
581A LEU* 2.9 40.0 + - - -
594A HIS* 6.0 0.4 - - - -
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Residues in contact with LEU 572 (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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521A TRP* 3.3 27.4 - - + +
522A TRP* 3.5 7.8 - - - -
524A TYR* 3.6 33.2 - - + -
525A GLY* 3.6 21.8 - - - -
528A LEU* 4.1 6.7 - - + -
568A ILE* 2.7 46.2 + - + +
569A CYS 4.1 0.9 - - - +
571A GLY* 1.3 72.1 - - - +
573A MET* 1.3 59.1 + - - +
574A THR 3.2 5.1 + - - -
580A ARG* 3.2 27.6 - - - -
581A LEU* 3.8 30.5 - - + +
591A VAL* 5.0 2.0 - - + -
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Residues in contact with MET 573 (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 TRP* 3.2 42.9 - - + +
525A GLY 4.1 8.5 - - - +
526A VAL* 3.8 26.2 - - + -
529A TYR* 3.9 33.7 - - + -
537A PRO* 3.8 15.9 - - - -
538A PHE* 4.2 3.0 - - + -
555A VAL* 4.1 15.7 - - + +
557A TYR* 3.9 14.7 + - - +
569A CYS* 2.7 32.4 + - + +
570A LYS* 3.7 6.0 - - - +
572A LEU* 1.3 73.9 - - - +
574A THR* 1.3 58.7 - - - +
575A LYS* 3.7 5.7 + - - +
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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