Contacts of the helix formed by residues 596 - 605 (chain A) 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 THR 596 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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590A CYS* 3.5 1.3 - - - -
594A GLY 4.3 6.1 - - - +
595A LEU* 1.3 73.5 - - - +
597A PRO* 1.3 72.3 - - - +
598A GLU* 3.2 28.4 + - - +
599A GLN* 3.0 42.6 + - + +
600A VAL* 3.1 13.0 + - - +
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Residues in contact with PRO 597 (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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559A HIS 5.3 7.0 - - - +
560A GLY 5.3 3.6 - - - +
561A LEU* 4.4 14.1 - - + -
586A LEU* 3.9 16.6 - - + +
590A CYS* 3.4 21.1 - - - -
595A LEU 4.3 0.2 - - - +
596A THR* 1.3 84.3 - - - +
598A GLU* 1.3 74.6 - - - +
600A VAL* 3.1 3.3 + - - +
601A VAL* 2.9 34.5 + - - +
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Residues in contact with GLU 598 (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* 5.5 0.2 - - - +
565A GLN* 4.0 23.6 + - - +
596A THR* 3.0 19.6 + - - +
597A PRO* 1.3 91.0 - - - +
599A GLN* 1.3 61.5 + - + +
601A VAL* 3.4 2.5 + - - +
602A ALA* 2.9 29.5 + - - +
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Residues in contact with GLN 599 (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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594A GLY 4.3 1.7 - - - +
595A LEU* 3.5 20.5 - - + +
596A THR* 3.0 43.1 + - + +
598A GLU* 1.3 75.7 - - + +
600A VAL* 1.3 56.8 + - - +
602A ALA* 3.2 7.7 + - - +
603A ILE* 2.8 35.6 + - - +
631A PRO* 5.0 1.2 - - - +
632A GLU* 4.2 21.8 - - - +
635A VAL* 3.5 42.1 - - + +
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Residues in contact with VAL 600 (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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582A VAL* 4.6 11.9 - - + -
586A LEU* 3.8 34.8 - - + +
589A LEU* 3.6 36.6 - - + -
590A CYS* 4.0 8.5 - - - -
595A LEU* 4.3 8.3 - - + -
596A THR 3.1 15.9 + - - +
597A PRO 3.1 6.0 + - - +
599A GLN* 1.3 77.6 - - - +
601A VAL* 1.3 57.0 + - + +
603A ILE* 3.3 10.6 + - - +
604A ALA* 2.9 27.4 + - - +
613A LEU* 3.9 7.5 - - + +
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Residues in contact with VAL 601 (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 30.1 - - + -
565A GLN* 3.9 34.8 - - + +
568A ALA* 4.9 2.7 - - + -
569A ILE* 3.6 32.1 - - + -
582A VAL* 5.8 1.1 - - + -
586A LEU* 5.4 1.3 - - + -
597A PRO 2.9 21.4 + - - +
598A GLU 4.0 3.8 - - - +
600A VAL* 1.3 77.9 - - + +
602A ALA* 1.3 56.4 + - - +
604A ALA 3.8 1.0 - - - +
605A SER* 2.5 42.2 + - - +
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Residues in contact with ALA 602 (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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598A GLU 2.9 18.0 + - - +
599A GLN* 3.3 10.1 - - - +
600A VAL 3.1 0.2 - - - -
601A VAL* 1.3 74.2 - - - +
603A ILE* 1.3 66.0 + - - +
605A SER* 3.4 13.5 + - - -
606A ASN* 3.5 13.9 + - - -
635A VAL* 5.3 2.2 - - + -
639A SER* 3.9 16.5 + - - +
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Residues in contact with ILE 603 (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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589A LEU* 5.0 0.2 - - + -
595A LEU* 4.3 18.6 - - + -
599A GLN 2.8 19.0 + - - +
600A VAL* 3.5 12.3 - - - +
602A ALA* 1.3 76.9 - - - +
604A ALA* 1.3 60.8 + - - +
605A SER 3.2 1.6 + - - -
606A ASN* 3.7 12.5 + - - +
609A GLY* 4.0 8.9 - - - -
612A ALA* 3.6 30.0 - - + +
613A LEU* 3.9 23.6 - - + +
616A VAL* 4.2 18.6 - - + -
635A VAL* 4.5 13.5 - - + -
638A ALA* 4.0 15.5 - - + +
639A SER* 4.0 14.8 + - - +
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Residues in contact with ALA 604 (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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569A ILE* 3.6 29.5 - - + +
572A HIS* 4.6 0.2 - - - -
578A ALA* 3.9 10.3 - - + +
582A VAL* 3.5 32.8 - - + -
600A VAL 2.9 12.7 + - - +
601A VAL 3.8 0.4 - - - +
602A ALA 3.3 0.2 - - - -
603A ILE* 1.3 75.8 - - - +
605A SER* 1.3 56.7 + - - +
606A ASN 3.2 13.8 + - - +
609A GLY* 4.2 5.2 - - - -
613A LEU* 3.6 17.3 - - + -
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Residues in contact with SER 605 (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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568A ALA* 3.7 13.3 - - - +
569A ILE* 3.7 13.2 + - - +
572A HIS* 2.9 30.2 + - - -
601A VAL* 2.5 34.0 + - - +
602A ALA* 3.9 7.2 - - - -
603A ILE 3.1 2.6 - - - -
604A ALA* 1.3 73.8 - - - +
606A ASN* 1.3 68.3 + - - +
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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