Contacts of the helix formed by residues 287 - 292 (chain A) in PDB entry 5I4E
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 GLU 287 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261A ARG* 2.9 53.9 + - + +
285A LEU* 4.5 1.6 - - - +
286A LEU* 1.3 72.1 - - - +
288A LYS* 1.3 62.2 + - - +
289A SER* 3.2 10.9 + - - +
290A ARG* 2.7 63.1 + - - +
301A PHE* 3.6 6.1 - - - -
491A GLU* 3.8 31.0 - - + +
492A GLN* 4.1 10.0 + - - -
495A ILE* 5.7 3.6 - - + -
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Residues in contact with LYS 288 (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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286A LEU* 2.9 23.1 + - + +
287A GLU* 1.3 70.7 - - - +
289A SER* 1.4 57.0 + - - +
291A ALA* 3.1 29.6 + - - +
301A PHE* 4.7 4.3 - - - -
442A ALA 5.5 0.8 + - - -
445A LYS* 3.3 46.9 - - + +
446A ALA* 4.5 10.3 - - - +
448A TYR* 5.5 1.3 - - + -
449A GLU* 3.1 46.2 + - + +
616A ASP* 2.8 41.7 + - - -
618A LEU* 5.9 1.4 - - - +
670A VAL* 6.1 0.2 - - - -
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Residues in contact with SER 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A GLU* 4.2 6.8 + - - +
288A LYS* 1.4 74.4 - - - +
290A ARG* 1.3 61.2 + - - +
291A ALA 3.1 5.4 - - - -
292A ILE* 3.1 24.1 + - - +
293A ARG* 3.2 14.2 + - - +
445A LYS* 3.6 22.4 - - - -
491A GLU* 3.0 33.5 + - - +
613A LYS* 4.8 10.0 + - - -
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Residues in contact with ARG 290 (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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251A ALA* 3.4 24.4 - - - +
252A LYS 3.6 11.3 + - - -
253A THR* 3.6 18.0 - - - +
261A ARG* 3.9 11.2 - - - +
287A GLU* 2.7 52.3 + - - +
289A SER* 1.3 76.7 + - - +
291A ALA* 1.4 58.4 + - - +
292A ILE 3.3 0.2 - - - -
293A ARG 3.6 7.6 - - - -
294A GLN* 2.8 35.0 + - + +
298A GLU* 2.8 32.9 + - - +
299A CYS 2.8 33.1 + - - +
300A SER* 3.0 16.6 + - - -
301A PHE* 4.1 9.2 - - + +
485A PHE* 5.3 4.0 - - - -
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Residues in contact with ALA 291 (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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288A LYS 3.1 16.9 + - - +
289A SER 3.1 1.0 - - - -
290A ARG* 1.4 79.8 - - - +
292A ILE* 1.3 61.5 + - + +
294A GLN* 4.2 0.3 + - - -
300A SER* 4.0 9.2 + - - -
301A PHE* 3.8 15.7 - - + -
304A PHE* 4.6 5.9 - - + -
329A PHE* 3.5 24.1 - - - +
330A LEU* 6.0 0.2 - - - +
372A VAL* 4.1 24.8 - - + +
373A LEU* 5.3 2.4 - - - +
444A ALA 4.9 1.6 - - - +
445A LYS* 4.9 0.7 - - + -
448A TYR* 4.2 12.3 - - + -
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Residues in contact with ILE 292 (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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289A SER* 3.2 19.5 - - - +
291A ALA* 1.3 81.7 - - + +
293A ARG* 1.4 86.1 + - + +
328A ARG 4.6 1.0 - - - +
329A PHE* 3.4 64.6 - - + +
331A THR* 4.4 0.9 + - - -
441A GLU* 3.7 32.3 - - + +
444A ALA* 4.3 5.4 - - + -
445A LYS* 3.8 36.6 - - + +
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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