Contacts of the helix formed by residues 593 - 600 (chain A) in PDB entry 4H1J
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 593 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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592A MET* 1.3 76.5 - - - +
594A PRO* 1.4 71.3 - - - +
595A GLU* 3.0 31.4 + - - -
596A SER* 2.9 24.3 + - - -
597A ILE* 3.0 20.9 + - - +
606A SER* 3.4 6.6 - - - -
609A TRP* 3.7 25.2 - - - +
610A MET* 4.8 2.8 - - - +
669A ARG* 3.9 6.5 - - - -
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Residues in contact with PRO 594 (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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593A SER* 1.4 85.8 - - - +
595A GLU* 1.4 61.1 + - - +
597A ILE* 3.9 1.9 - - + +
598A ASN* 2.9 36.9 + - - -
609A TRP* 3.5 34.8 - - + -
635A ILE* 3.8 19.5 - - + -
638A LEU* 4.4 10.7 - - + -
664A TYR* 3.5 46.7 - - + +
669A ARG* 4.0 2.7 - - - +
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Residues in contact with GLU 595 (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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593A SER* 3.0 16.4 + - - +
594A PRO* 1.4 78.7 - - - +
596A SER* 1.4 58.6 + - - +
599A PHE* 3.0 36.0 + - + +
600A ARG 3.4 4.9 + - - -
601A ARG* 3.4 53.7 + - + +
603A THR* 4.6 5.1 + - + +
606A SER* 3.5 11.9 + - - -
664A TYR* 4.2 2.8 - - - +
666A PRO* 3.6 15.8 - - + +
669A ARG* 2.7 44.0 + - - -
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Residues in contact with SER 596 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592A MET* 3.6 22.4 - - - +
593A SER* 2.9 26.6 + - - -
595A GLU* 1.4 73.2 - - - +
597A ILE* 1.4 60.6 + - - +
600A ARG* 3.0 26.4 + - - +
601A ARG 2.7 25.4 + - - +
602A PHE* 3.5 29.0 - - - -
606A SER* 3.6 6.1 - - - -
610A MET* 6.0 0.5 - - - +
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Residues in contact with ILE 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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589A ILE* 3.6 45.0 - - + +
592A MET* 3.7 34.5 - - + +
593A SER 3.0 15.1 + - - +
594A PRO 4.0 3.4 - - - +
596A SER* 1.4 77.8 - - - +
598A ASN* 1.4 64.1 + - - +
600A ARG* 4.7 8.5 + - - +
634A VAL* 4.1 13.9 - - + -
635A ILE* 3.9 31.4 - - + -
638A LEU* 4.2 9.6 - - + -
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Residues in contact with ASN 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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594A PRO 2.9 26.0 + - - +
597A ILE* 1.4 76.3 - - - +
599A PHE* 1.3 89.2 + - + +
600A ARG* 5.7 0.8 - - - +
635A ILE* 3.5 23.3 - - - +
639A GLU* 3.2 25.9 + - - +
664A TYR* 3.7 8.5 + - - -
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Residues in contact with PHE 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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595A GLU* 3.0 19.8 + - + +
598A ASN* 1.3 103.3 - - + +
600A ARG* 1.4 72.9 + - - +
601A ARG* 3.2 35.2 + - + +
664A TYR* 5.7 2.2 - - - -
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Residues in contact with ARG 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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584A VAL* 3.4 26.7 + - - +
587A LEU* 3.4 28.5 - - - +
592A MET* 5.1 1.3 - - - +
596A SER 3.0 25.3 + - - -
597A ILE 4.8 7.7 + - - +
598A ASN 5.7 0.4 - - - -
599A PHE* 1.4 78.9 - - - +
601A ARG* 1.3 61.0 + - - +
602A PHE* 3.5 25.8 + - + -
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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