Contacts of the helix formed by residues 562 - 569 (chain B) in PDB entry 1IT8
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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358B GLU* 3.4 38.4 + - - -
359B PHE* 4.1 0.8 - - - -
538B ILE 3.5 12.8 - - - -
539B ARG* 5.0 0.4 - - - -
540B PRO* 4.1 13.1 - - - +
561B LEU* 1.3 75.1 - - - +
563B GLY* 1.3 70.7 + - - +
564B ARG 3.8 0.2 + - - -
565B GLU* 2.8 44.7 + - - +
566B MET* 3.0 9.6 + - - +
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Residues in contact with GLY 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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534B ALA* 4.2 6.6 - - - +
535B ASP 3.3 25.6 - - - -
536B PRO* 4.5 1.3 + - - -
538B ILE* 3.0 23.6 + - - +
562B SER* 1.3 70.8 - - - +
564B ARG* 1.3 64.3 + - - +
566B MET* 2.9 25.5 + - - +
567B ILE* 3.4 11.8 + - - +
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Residues in contact with ARG 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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217B LYS 4.3 6.0 + - - -
218B MET* 3.2 28.8 + - - +
219B ALA 4.7 1.4 + - - -
220B LEU 3.2 21.6 + - - -
221B ARG* 5.1 0.2 - - - +
222B PRO* 3.7 25.5 - - + +
355B PHE* 5.4 2.2 - - - -
358B GLU* 3.0 42.0 + - - +
359B PHE* 3.9 14.5 - - - -
536B PRO* 4.6 12.2 + - + +
562B SER* 3.3 0.6 + - - -
563B GLY* 1.3 72.4 - - - +
565B GLU* 1.3 61.6 + - - +
567B ILE* 3.5 20.0 + - - +
568B VAL* 3.5 17.0 + - + +
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Residues in contact with GLU 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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12B ILE* 4.1 10.0 - - - +
15B ARG* 2.7 44.4 + - - -
20B ARG* 4.6 4.0 + - - -
222B PRO* 3.9 24.0 - - + +
359B PHE* 3.6 15.0 - - + -
561B LEU* 3.8 12.9 - - + -
562B SER* 2.8 37.7 + - - +
564B ARG* 1.3 68.3 - - + +
566B MET* 1.3 66.0 + - - +
567B ILE 3.0 2.8 + - - -
568B VAL* 3.2 7.7 + - - +
569B PHE* 2.9 38.0 + - + +
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Residues in contact with MET 566 (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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510B VAL* 3.5 30.7 - - + -
528B ALA* 3.1 14.7 - - - +
531B VAL* 3.8 15.6 - - + +
534B ALA* 4.0 3.6 - - + -
538B ILE* 3.4 49.1 - - + -
559B ALA* 4.1 9.0 - - + -
561B LEU* 3.8 24.4 - - + +
562B SER 3.0 11.1 + - - +
563B GLY* 2.9 15.9 + - - +
565B GLU* 1.3 75.4 - - - +
567B ILE* 1.3 62.1 - - - +
569B PHE 3.8 2.9 - - - +
574B ALA* 3.9 26.2 - - + +
575B VAL* 4.0 0.9 - - - -
601B MG 3.1 12.0 - - - -
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Residues in contact with ILE 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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531B VAL* 4.1 5.7 - - + +
532B ILE 3.8 19.3 - - - +
533B PHE* 4.0 19.1 - - + +
534B ALA* 3.6 36.1 - - + +
536B PRO* 6.3 0.7 - - + -
563B GLY 3.5 12.8 - - - +
564B ARG* 3.5 13.2 - - - +
565B GLU 3.0 0.6 - - - -
566B MET* 1.3 76.8 - - - +
568B VAL* 1.3 63.4 + - + +
570B GLN* 4.0 2.4 + - - -
601B MG 2.3 27.2 - - - -
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Residues in contact with VAL 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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221B ARG* 4.3 16.7 + - + +
222B PRO* 4.0 26.2 - - + -
223B ASP* 3.4 28.9 - - - +
564B ARG* 3.5 17.0 + - + +
565B GLU* 3.4 14.8 - - - +
567B ILE* 1.3 78.8 - - + +
569B PHE* 1.3 72.7 + - + +
570B GLN* 3.5 11.8 + - - +
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Residues in contact with PHE 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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10B PHE* 3.9 22.9 - + - -
11B GLU* 4.9 2.2 - - - -
12B ILE* 3.7 36.1 - - + -
20B ARG* 4.5 0.2 - - - -
222B PRO* 3.4 17.3 - - + -
223B ASP* 3.4 33.2 - - + -
528B ALA* 3.1 29.3 - - + +
561B LEU* 4.1 11.9 - - + -
565B GLU* 2.9 46.6 + - + +
567B ILE 3.4 0.4 - - - -
568B VAL* 1.3 79.2 - - + +
570B GLN* 1.3 60.4 + - - +
571B TYR* 3.6 17.5 - + - +
601B MG 2.9 23.0 - - - -
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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