Contacts of the helix formed by residues 562 - 573 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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437B GLU* 2.6 42.6 + - - -
560B SER 3.8 0.6 + - - -
561B LEU* 1.3 79.7 - - - +
563B LYS* 1.3 62.1 + - - +
564B GLU* 3.9 7.6 - - - -
565B ALA* 2.8 19.0 + - - +
566B VAL* 3.3 23.7 + - - +
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Residues in contact with LYS 563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562B SER* 1.3 74.1 - - - +
564B GLU* 1.3 86.7 + - - +
565B ALA 3.3 0.4 - - - -
566B VAL* 3.9 5.4 - - - +
567B SER* 2.9 34.0 + - - -
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Residues in contact with GLU 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437B GLU* 4.5 4.9 - - - +
562B SER* 3.9 6.8 + - - +
563B LYS* 1.3 104.7 + - - +
565B ALA* 1.3 67.2 + - - +
567B SER* 4.3 0.4 - - - -
568B ILE 3.1 15.2 + - - -
594B HIS* 3.4 10.3 - - + -
595B ALA* 3.3 38.9 - - + +
596B PHE* 3.3 27.5 - - + +
598B ARG* 4.8 10.7 + - - -
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Residues in contact with ALA 565 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437B GLU* 4.0 5.6 - - - +
532B LEU* 3.4 24.2 - - + -
561B LEU* 4.2 8.5 - - + -
562B SER* 2.8 32.1 + - - +
564B GLU* 1.3 79.8 - - - +
566B VAL* 1.3 63.5 + - - +
567B SER 2.9 1.7 + - - -
568B ILE* 3.0 17.2 + - - +
569B CYS* 3.3 10.6 + - - -
596B PHE* 3.6 14.5 - - + -
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Residues in contact with VAL 566 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557B TYR* 3.6 42.6 - - + -
558B PRO 5.5 0.9 - - - +
559B LYS* 6.2 1.8 - - - -
561B LEU* 3.9 14.8 - - + +
562B SER 3.3 19.4 + - - +
563B LYS* 4.2 5.4 - - - +
565B ALA* 1.3 78.2 - - - +
567B SER* 1.3 59.2 + - - +
569B CYS* 3.8 2.1 + - - +
570B LYS* 3.2 46.4 + - + +
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Residues in contact with SER 567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563B LYS* 2.9 24.9 + - - -
564B GLU* 3.8 2.2 - - - -
565B ALA 2.9 1.8 + - - -
566B VAL* 1.3 77.7 - - - +
568B ILE* 1.3 63.3 + - - -
569B CYS 3.2 0.2 - - - -
570B LYS* 3.5 9.4 + - - +
571B GLY* 3.1 18.2 + - - -
594B HIS* 2.8 24.2 + - - -
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Residues in contact with ILE 568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524B TYR* 4.9 0.4 - - + -
528B LEU* 4.2 13.7 - - + -
564B GLU 3.1 12.0 + - - +
565B ALA* 3.0 22.1 + - - +
567B SER* 1.3 75.1 - - - +
569B CYS* 1.3 64.3 + - - +
571B GLY* 3.1 2.0 + - - +
572B LEU* 2.8 51.7 + - + +
581B LEU* 3.8 15.7 - - + +
591B VAL* 4.9 4.5 - - + -
594B HIS* 3.2 20.6 + - + +
596B PHE* 3.5 41.5 - - + -
597B PHE* 4.0 19.5 - - + -
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Residues in contact with CYS 569 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525B GLY 4.8 2.0 - - - -
528B LEU* 4.3 16.4 - - - -
529B TYR* 4.3 22.9 - - - -
532B LEU* 4.6 6.1 - - - -
557B TYR* 3.2 32.8 - - + +
561B LEU* 6.4 1.1 - - - -
565B ALA 3.3 15.2 + - - +
566B VAL 4.1 0.4 - - - +
567B SER 3.2 0.4 - - - -
568B ILE* 1.3 86.1 - - - +
570B LYS* 1.3 55.5 + - - +
572B LEU* 4.4 5.4 - - - +
573B MET* 2.5 48.6 + - + +
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Residues in contact with LYS 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557B TYR* 3.1 25.7 + - + +
566B VAL* 3.2 36.5 + - + +
567B SER* 3.5 9.2 + - - +
568B ILE 3.4 0.2 - - - -
569B CYS* 1.3 75.5 - - - +
571B GLY* 1.3 53.0 + - - +
573B MET 3.4 2.9 - - - -
574B THR* 2.5 41.1 + - - -
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Residues in contact with GLY 571 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567B SER 3.1 12.4 + - - -
568B ILE 3.1 4.7 + - - -
570B LYS* 1.3 79.3 - - - +
572B LEU* 1.3 54.5 + - - +
574B THR* 3.2 12.8 + - - -
579B LYS 5.9 0.2 - - - -
580B ARG* 3.4 1.6 - - - +
581B LEU* 2.5 47.2 + - - -
594B HIS* 6.1 0.2 - - - -
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Residues in contact with LEU 572 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521B TRP* 3.7 16.2 - - + +
522B TRP* 3.8 9.2 - - - -
524B TYR* 3.7 31.2 - - + -
525B GLY* 3.6 30.3 - - - -
528B LEU* 3.9 11.2 - - + -
568B ILE* 2.8 39.8 + - + +
569B CYS* 3.9 3.4 - - - +
571B GLY* 1.3 72.7 - - - +
573B MET* 1.3 61.0 + - - +
574B THR 3.2 4.5 - - - -
580B ARG* 3.2 30.0 + - - +
581B LEU* 3.8 28.9 - - + +
591B VAL* 4.9 3.1 - - + -
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Residues in contact with MET 573 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522B TRP* 3.4 26.6 - - + +
525B GLY* 4.1 15.3 - - - +
526B VAL* 4.1 14.8 - - + +
529B TYR* 3.8 35.7 - - + -
537B PRO* 3.6 29.8 - - + -
538B PHE* 4.1 12.0 - - - -
555B VAL* 4.1 12.5 - - + +
557B TYR* 4.1 9.9 - - - +
569B CYS* 2.5 37.7 + - + +
570B LYS* 3.4 5.7 - - - -
572B LEU* 1.3 72.5 - - - +
574B THR* 1.3 59.8 + - - +
575B LYS* 3.5 6.8 + - - +
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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