Contacts of the helix formed by residues 562 - 573 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437C GLU* 2.7 30.0 + - - -
560C SER 3.4 4.7 + - - -
561C LEU* 1.3 75.7 - - - +
563C LYS* 1.3 57.1 + - - +
564C GLU* 2.7 29.6 + - - -
565C ALA* 3.0 19.1 + - - +
566C VAL* 3.0 13.0 + - - +
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Residues in contact with LYS 563 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561C LEU 3.8 1.9 + - - -
562C SER* 1.3 74.4 + - - +
564C GLU* 1.3 88.3 + - - +
566C VAL* 4.1 7.5 - - - +
567C SER* 3.0 23.9 + - - -
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Residues in contact with GLU 564 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437C GLU* 4.0 1.0 - - - +
562C SER* 2.7 20.5 + - - +
563C LYS* 1.3 105.4 + - + +
565C ALA* 1.3 58.3 + - - +
567C SER* 3.5 7.4 - - - -
568C ILE 3.1 21.7 + - - -
594C HIS* 3.5 7.3 - - - -
595C ALA* 3.7 30.5 - - + +
596C PHE* 3.6 28.6 - - + +
598C ARG* 3.3 30.4 + - - +
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Residues in contact with ALA 565 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437C GLU* 3.9 11.0 - - - +
532C LEU* 3.5 27.8 - - + -
561C LEU* 4.4 7.9 - - + -
562C SER* 3.0 18.2 + - - +
564C GLU* 1.3 73.9 - - - +
566C VAL* 1.3 66.8 + - - +
567C SER 3.1 1.3 - - - -
568C ILE* 3.1 5.4 + - - +
569C CYS* 3.0 26.1 + - - -
596C PHE* 3.5 17.8 - - + -
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Residues in contact with VAL 566 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557C TYR* 3.8 32.8 - - + -
558C PRO 5.6 0.2 - - - +
561C LEU* 3.8 24.5 - - + +
562C SER 3.0 18.6 + - - +
563C LYS* 4.1 6.5 - - - +
565C ALA* 1.3 75.1 - - - +
567C SER* 1.3 64.4 + - - +
569C CYS* 3.2 1.6 + - - +
570C LYS* 3.0 53.9 + - + +
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Residues in contact with SER 567 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563C LYS 3.0 18.6 + - - -
564C GLU* 3.5 8.1 - - - -
566C VAL* 1.3 79.5 - - - +
568C ILE* 1.3 63.5 + - - +
570C LYS* 3.2 6.0 + - - +
571C GLY* 3.0 18.2 + - - -
594C HIS* 2.9 22.3 + - - -
595C ALA* 6.4 0.2 - - - -
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Residues in contact with ILE 568 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524C TYR* 5.5 0.7 - - + -
528C LEU* 3.9 23.6 - - + -
564C GLU 3.1 13.2 + - - +
565C ALA* 3.1 13.9 + - - +
567C SER* 1.3 78.3 - - - +
569C CYS* 1.3 65.2 + - - +
571C GLY* 3.0 2.3 + - - +
572C LEU* 2.8 41.1 + - + +
581C LEU* 3.8 18.2 - - + -
591C VAL* 5.1 2.5 - - + -
594C HIS* 3.5 20.2 - - + +
596C PHE* 3.7 29.2 - - + -
597C PHE* 3.5 34.3 - - + -
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Residues in contact with CYS 569 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525C GLY* 5.5 0.7 - - - -
528C LEU* 4.6 7.9 - - - -
529C TYR* 4.4 20.9 - - - -
532C LEU* 4.6 8.7 - - - -
557C TYR* 3.2 34.8 - - + +
561C LEU* 6.1 1.1 - - - -
565C ALA 3.0 20.8 + - - +
566C VAL 3.7 0.2 - - - +
568C ILE* 1.3 86.5 - - - +
570C LYS* 1.3 56.9 + - - +
572C LEU* 3.4 3.1 + - - +
573C MET* 2.8 53.2 + - + +
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Residues in contact with LYS 570 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557C TYR* 3.4 27.1 - - + +
566C VAL* 3.0 39.9 + - + +
567C SER* 3.8 4.9 - - - +
569C CYS* 1.3 77.2 - - - +
571C GLY* 1.3 55.0 + - - +
573C MET* 3.6 3.6 - - - -
574C THR* 2.5 37.0 + - - -
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Residues in contact with GLY 571 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567C SER 3.0 10.1 + - - -
568C ILE 3.0 7.0 + - - -
570C LYS* 1.3 77.3 - - - +
572C LEU* 1.3 55.4 + - - +
574C THR* 3.1 16.7 + - - -
579C LYS 4.4 0.6 - - - +
580C ARG* 3.6 0.7 - - - +
581C LEU* 2.8 43.1 + - - -
594C HIS* 6.0 0.4 - - - -
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Residues in contact with LEU 572 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521C TRP* 3.3 32.8 - - + +
522C TRP* 3.5 6.4 - - - -
524C TYR* 3.2 38.4 - - + -
525C GLY* 3.6 21.5 - - - -
528C LEU* 4.1 9.2 - - + -
568C ILE* 2.8 30.0 + - + +
569C CYS* 4.0 2.7 - - - +
571C GLY* 1.3 78.6 - - - +
573C MET* 1.3 57.2 + - - +
574C THR 3.3 0.9 - - - -
580C ARG* 3.4 24.4 + - - -
581C LEU* 3.6 31.9 - - + +
591C VAL* 5.2 1.1 - - + -
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Residues in contact with MET 573 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522C TRP* 3.2 39.7 - - + +
525C GLY* 2.9 36.3 - - - +
526C VAL* 4.0 11.7 - - + +
529C TYR* 3.7 16.4 - - + -
537C PRO* 3.8 31.2 - - - -
538C PHE* 4.3 1.9 - - - -
555C VAL* 4.0 19.5 - - + +
557C TYR* 4.7 2.0 - - - +
569C CYS* 2.8 37.7 + - + +
570C LYS* 3.4 6.1 + - - -
572C LEU* 1.3 72.9 - - - +
574C THR* 1.3 58.8 + - - +
575C LYS* 3.6 7.3 + - - +
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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