Contacts of the helix formed by residues 592 - 599 (chain A) in PDB entry 4EJX
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 ASP 592 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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396A ARG* 5.1 2.3 + - - -
589A ASP* 3.1 30.7 + - + +
590A LYS 3.3 2.0 - - - -
591A GLU* 1.3 79.2 - - - +
593A GLU* 1.3 68.2 + - - +
594A ASP* 3.5 23.9 + - - +
595A PHE* 3.8 10.5 + - + +
596A GLN* 3.2 31.3 + - - +
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Residues in contact with GLU 593 (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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591A GLU 4.3 2.7 + - - +
592A ASP* 1.3 80.1 + - - +
594A ASP* 1.3 62.5 + - - +
596A GLN* 4.1 15.9 - - - +
597A GLU* 3.8 21.8 + - - +
931A GLU* 5.5 3.6 - - - +
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Residues in contact with ASP 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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388A VAL* 5.2 9.4 - - - +
396A ARG* 3.0 28.3 + - - +
592A ASP* 3.3 15.4 + - - +
593A GLU* 1.3 77.7 - - - +
595A PHE* 1.3 63.6 + - - +
596A GLN 3.4 0.4 + - - -
597A GLU* 3.8 6.6 + - - +
598A SER* 3.8 10.6 + - - -
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Residues in contact with PHE 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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395A THR* 3.4 28.0 - - - -
396A ARG* 3.5 17.9 - - - +
397A ILE* 5.1 7.2 - - + -
569A ASN* 3.6 8.1 - - - -
574A LEU* 4.8 5.8 - - + -
578A ILE* 4.6 9.9 - - + -
588A VAL* 3.7 27.1 - - + -
589A ASP* 3.3 29.2 - - + +
590A LYS* 4.3 17.3 - - + -
592A ASP* 3.5 14.2 + - + +
594A ASP* 1.3 78.0 - - - +
596A GLN* 1.3 64.9 + - - +
598A SER* 2.7 26.2 + - - -
599A ASN* 3.2 36.7 + - - -
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Residues in contact with GLN 596 (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 ASN* 2.7 45.2 + - - +
570A GLU* 5.7 3.0 + - - -
590A LYS 3.9 19.0 + - - +
591A GLU* 5.5 5.3 + - - +
592A ASP 3.2 18.2 + - - +
593A GLU* 4.3 17.6 - - - +
594A ASP 3.4 0.2 - - - -
595A PHE* 1.3 79.3 - - + +
597A GLU* 1.3 56.0 + - - +
598A SER 3.3 0.2 + - - -
599A ASN 3.4 0.2 + - - -
600A LYS* 3.1 30.3 + - - +
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Residues in contact with GLU 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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388A VAL* 5.6 6.7 - - + +
389A PHE* 3.3 24.1 - - - -
593A GLU 3.8 14.5 + - - +
594A ASP* 3.8 7.5 + - - +
595A PHE 3.3 0.6 - - - -
596A GLN* 1.3 75.1 - - - +
598A SER* 1.3 58.9 + - - +
600A LYS* 3.2 46.3 + - + +
602A HIS* 4.1 12.7 + - - -
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Residues in contact with SER 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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388A VAL* 3.9 18.6 - - - -
389A PHE* 3.9 11.0 - - - +
396A ARG* 3.7 35.0 - - - -
397A ILE 5.5 1.5 + - - -
401A TYR* 3.6 3.3 + - - -
594A ASP 3.8 5.4 + - - -
595A PHE* 2.7 23.2 + - - -
596A GLN 3.2 0.2 - - - -
597A GLU* 1.3 76.7 - - - +
599A ASN* 1.3 78.7 + - - +
600A LYS 3.3 8.7 - - - +
601A MET* 3.6 16.5 - - - +
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Residues in contact with ASN 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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397A ILE* 3.8 18.7 + - - +
401A TYR* 3.3 18.3 + - - -
566A PHE 3.0 15.1 - - - +
568A GLU* 3.4 20.3 + - + +
569A ASN* 2.8 43.5 + - - +
574A LEU* 3.8 12.0 - - - +
595A PHE* 3.2 28.3 + - - -
596A GLN 3.4 1.6 + - - -
598A SER* 1.3 86.8 + - - +
600A LYS* 1.3 62.2 + - - +
601A MET* 3.2 9.5 + - - +
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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