Contacts of the helix formed by residues 392 - 399 (chain A) in PDB entry 1EJD
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 ILE 392 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A ASP* 3.3 21.9 + - + +
3A LYS 3.7 11.9 - - - +
4A PHE* 3.3 61.9 - - + +
373A SER* 4.7 1.3 - - - -
389A VAL* 3.2 38.4 - - + +
390A ASP 4.2 0.2 - - - -
391A ARG* 1.3 72.0 - - - +
393A TYR* 1.3 65.0 + - - +
394A HIS 3.0 2.9 - - - -
395A ILE* 2.9 23.7 + - + +
396A ASP* 3.0 14.6 + - - +
415A ARG* 3.6 18.2 - - + +
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Residues in contact with TYR 393 (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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1A MET* 3.7 33.4 - - + -
2A ASP* 4.9 4.1 + - + +
391A ARG* 3.1 37.4 + - + -
392A ILE* 1.3 80.4 - - - +
394A HIS* 1.3 95.1 + + - +
396A ASP* 3.7 13.7 - - + +
397A ARG* 3.1 60.4 + - - +
2436A PO4 4.2 8.0 + - - -
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Residues in contact with HIS 394 (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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367A ALA 3.8 12.6 - - - -
368A THR* 3.2 44.8 + - + +
370A LEU* 3.3 25.4 - - - +
373A SER* 4.7 6.7 - - - -
391A ARG* 3.2 30.2 + - + +
392A ILE 3.0 0.2 - - - -
393A TYR* 1.3 111.5 + + - +
395A ILE* 1.3 61.5 + - - +
397A ARG* 3.4 10.0 + - - +
398A GLY 3.7 1.9 + - - -
2436A PO4 2.6 45.6 + - - +
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Residues in contact with ILE 395 (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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4A PHE* 4.3 10.3 - - + -
370A LEU* 3.7 8.2 - - - +
373A SER* 3.2 39.3 - - - +
374A ALA* 3.7 8.1 - - - +
377A VAL* 3.5 31.9 - - + -
392A ILE* 2.9 16.4 + - + +
394A HIS* 1.3 78.4 - - - +
396A ASP* 1.3 59.5 + - - +
398A GLY* 2.9 5.4 + - - -
399A TYR* 2.9 46.4 + - + +
402A ILE* 3.7 29.2 - - + +
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Residues in contact with ASP 396 (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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2A ASP* 5.2 0.7 - - - +
4A PHE* 4.3 7.8 - - - -
47A LEU* 3.4 19.2 - - - +
48A LYS 5.3 0.7 + - - -
392A ILE* 3.0 19.1 + - - +
393A TYR* 3.3 16.3 + - + +
395A ILE* 1.3 78.8 - - - +
397A ARG* 1.3 64.3 + - + +
399A TYR 3.4 8.7 - - - +
401A ARG* 5.5 4.0 + - - -
402A ILE 5.6 1.2 + - - -
403A GLU* 4.7 0.7 - - - +
415A ARG* 2.8 46.1 + - - -
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Residues in contact with ARG 397 (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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22A LYS* 3.3 24.5 + - - +
47A LEU* 3.8 16.3 - - - +
48A LYS* 2.8 61.9 + - + +
49A ASP* 5.3 2.4 + - - +
393A TYR* 3.1 53.8 + - - +
394A HIS 3.7 5.6 - - - +
395A ILE 3.0 1.2 + - - -
396A ASP* 1.3 81.1 - - - +
398A GLY* 1.3 56.5 + - - +
2436A PO4 3.6 26.1 + - - +
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Residues in contact with GLY 398 (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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22A LYS* 4.6 9.4 - - - +
47A LEU* 4.2 13.8 - - - +
231A ASP* 4.2 14.4 - - - +
370A LEU* 3.9 21.9 - - - +
371A ARG* 4.7 5.5 + - - -
394A HIS 3.7 3.4 + - - -
395A ILE 2.9 4.1 + - - -
397A ARG* 1.3 81.5 - - - +
399A TYR* 1.3 68.1 + - - +
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Residues in contact with TYR 399 (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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47A LEU* 3.8 3.4 - - - -
234A GLU* 4.0 31.9 - - + +
237A THR* 2.8 41.1 + - + +
238A PHE* 5.0 1.1 - + - -
309A GLN* 4.1 1.0 + - - -
370A LEU* 3.5 26.0 - - + -
371A ARG* 3.0 37.2 + - - -
374A ALA* 3.8 21.8 - - + +
395A ILE* 2.9 19.5 + - + +
396A ASP* 3.4 18.4 - - - +
397A ARG 3.8 0.2 - - - -
398A GLY* 1.3 79.4 - - - +
400A GLU* 1.3 61.0 + - - +
401A ARG* 3.1 8.3 + - - -
402A ILE* 3.8 33.7 + - + -
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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