Contacts of the helix formed by residues 574 - 584 (chain B) in PDB entry 4OSI
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 GLY 574 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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539B GLY 4.2 3.4 + - - -
572B HIS 3.4 0.4 + - - -
573B ASP* 1.3 73.5 - - - +
575B GLY* 1.3 63.3 + - - +
576B LYS 3.3 2.0 - - - -
577B GLN* 3.5 8.1 + - - +
578B ALA* 3.2 19.8 + - - +
608B GLY 5.6 0.3 + - - -
609B GLY 5.5 2.3 + - - -
610B LYS 5.5 0.5 + - - -
11G T 3.6 48.7 + - - +
12G C 3.9 7.2 + - - -
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Residues in contact with GLY 575 (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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540B GLY 5.9 1.0 + - - -
544B ALA* 4.9 3.5 - - - +
569B ILE 3.8 17.7 - - - -
570B ALA* 4.2 11.0 - - - -
572B HIS* 2.9 19.5 + - - -
573B ASP 4.2 0.7 - - - -
574B GLY* 1.3 76.1 - - - +
576B LYS* 1.3 57.7 + - - +
578B ALA* 2.8 21.1 + - - +
579B LEU* 2.9 20.7 + - - +
11G T 4.8 0.8 + - - -
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Residues in contact with LYS 576 (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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543B GLN* 3.0 54.3 - - + +
544B ALA* 4.2 8.1 - - - +
547B THR* 3.1 36.8 - - + +
550B ARG* 5.8 0.4 - - - +
574B GLY 3.3 0.4 - - - -
575B GLY* 1.3 72.7 - - - +
577B GLN* 1.3 82.4 + - - +
578B ALA 3.0 0.7 + - - -
579B LEU* 3.1 3.1 + - - +
580B GLU* 2.9 43.9 + - - +
11G T 3.8 9.6 + - - +
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Residues in contact with GLN 577 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574B GLY 3.6 8.3 - - - +
575B GLY 3.4 0.2 - - - -
576B LYS* 1.3 90.4 - - - +
578B ALA* 1.3 56.3 + - - +
580B GLU* 3.8 10.4 + - - +
581B THR* 2.7 37.8 + - - -
610B LYS* 3.4 35.9 + - + +
11G T 3.0 43.6 + - - +
12G C 3.7 21.1 - - - +
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Residues in contact with ALA 578 (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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569B ILE* 3.5 27.6 - - + +
574B GLY 3.2 9.8 + - - +
575B GLY* 2.8 16.1 + - - +
577B GLN* 1.3 78.6 - - - +
579B LEU* 1.3 67.5 + - - +
581B THR* 3.8 1.0 - - - -
582B VAL* 2.9 23.7 + - - +
604B ALA* 3.9 12.6 - - + +
606B ASN 5.5 1.1 - - - +
609B GLY* 4.5 3.1 - - - +
610B LYS 4.1 17.4 - - - +
613B LEU* 4.4 0.4 - - - +
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Residues in contact with LEU 579 (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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544B ALA 4.5 0.4 - - - +
547B THR* 3.4 33.2 - - + +
548B VAL* 3.5 35.0 - - + +
551B LEU* 4.4 12.6 - - + -
555B LEU* 5.2 7.0 - - + +
566B VAL* 4.2 18.4 - - + +
569B ILE* 3.7 32.3 - - + -
570B ALA* 3.6 15.5 - - + +
575B GLY 2.9 17.4 + - - +
576B LYS 3.5 0.9 - - - +
578B ALA* 1.3 74.1 - - - +
580B GLU* 1.3 64.2 + - - +
582B VAL* 3.0 6.6 + - + +
583B GLN* 2.9 20.8 + - - +
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Residues in contact with GLU 580 (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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547B THR* 4.3 8.5 - - + -
550B ARG* 2.9 31.9 + - - +
551B LEU* 4.2 5.8 - - + +
576B LYS* 2.9 44.4 + - - +
577B GLN* 3.8 11.8 + - - +
579B LEU* 1.3 71.4 - - - +
581B THR* 1.3 64.2 + - - +
582B VAL 3.0 0.3 + - - -
583B GLN* 3.0 16.6 + - - +
584B ARG* 2.9 30.2 + - - +
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Residues in contact with THR 581 (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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577B GLN* 2.7 25.1 + - - -
580B GLU* 1.3 73.6 - - - +
582B VAL* 1.3 57.0 + - - +
584B ARG* 3.5 16.5 + - - +
585B LEU* 2.9 41.4 + - + +
610B LYS* 3.2 27.8 - - - +
613B LEU* 3.8 23.3 - - + -
614B GLU* 3.8 31.4 - - + +
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Residues in contact with VAL 582 (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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555B LEU* 4.4 12.1 - - + -
561B LEU* 5.3 4.7 - - + -
569B ILE* 5.3 11.0 - - + -
578B ALA 2.9 11.3 + - - +
579B LEU* 3.4 9.9 - - + +
581B THR* 1.3 72.8 - - - +
583B GLN* 1.3 56.8 + - - +
584B ARG 2.7 15.2 + - - -
585B LEU* 2.8 12.1 + - - -
586B LEU* 2.9 37.4 + - + +
600B VAL* 4.3 13.7 - - + +
601B VAL* 5.8 1.6 - - + +
604B ALA* 3.7 19.3 - - + -
613B LEU* 3.4 27.6 - - + -
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Residues in contact with GLN 583 (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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550B ARG* 5.1 4.6 + - - +
551B LEU* 4.1 30.6 - - + +
554B VAL* 4.1 25.2 - - + +
555B LEU* 3.3 30.3 - - + -
559B HIS* 4.3 14.5 + - + -
579B LEU 2.9 16.1 + - - +
580B GLU* 3.3 12.1 - - - +
582B VAL* 1.3 71.3 - - - +
584B ARG* 1.3 66.5 + - - +
586B LEU 5.0 0.4 - - - -
587B PRO* 5.0 3.6 - - - +
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Residues in contact with ARG 584 (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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580B GLU* 2.9 17.1 + - - +
581B THR* 4.0 18.6 + - - +
582B VAL 2.8 1.0 - - - -
583B GLN* 1.3 91.0 - - - +
585B LEU* 1.3 83.0 + - - +
587B PRO* 4.1 8.4 - - - +
614B GLU* 4.5 14.6 + - - +
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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