Contacts of the helix formed by residues 395 - 400 (chain B) in PDB entry 4H3I
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 GLY 395 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B ASP 3.2 11.0 - - - -
292B THR* 3.2 16.8 - - - -
294B ASN 3.2 12.7 + - - -
295B LEU* 4.4 1.4 - - - +
393B VAL 3.1 8.7 + - - -
394B MET* 1.3 77.0 - - - +
396B ALA* 1.3 67.8 + - - -
397B VAL 3.1 3.6 - - - -
398B ILE* 2.9 13.2 + - - +
399B MET* 3.0 13.0 + - - +
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Residues in contact with ALA 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B SER* 3.7 30.3 - - - +
75B TYR* 4.6 9.2 - - + -
215B LEU* 4.6 7.4 - - + -
289B ASP 4.1 1.6 + - - -
290B SER* 5.1 5.1 - - - +
292B THR 2.8 13.5 + - - +
293B THR* 3.3 11.4 + - - +
395B GLY* 1.3 70.7 - - - -
397B VAL* 1.3 56.7 + - - +
399B MET* 3.7 9.6 - - - -
400B GLU* 2.8 41.3 + - + +
503B 10V 5.6 1.1 - - - +
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Residues in contact with VAL 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B SER* 5.3 2.2 - - - -
293B THR* 3.1 18.9 + - + +
294B ASN* 3.8 1.3 - - - -
295B LEU* 3.8 23.1 - - + +
361B ILE* 3.9 18.1 - - + +
365B GLN* 3.5 42.3 - - - +
366B TYR* 3.9 13.2 - - + -
368B ARG* 6.0 1.6 - - + -
384B ALA* 3.3 40.8 - - + +
395B GLY 3.1 0.4 - - - -
396B ALA* 1.3 77.0 - - - +
398B ILE* 1.3 64.0 + - - +
400B GLU* 4.1 5.6 + - - +
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Residues in contact with ILE 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B LEU* 3.8 28.0 - - + -
344B ILE* 6.4 0.2 - - + -
346B LEU* 3.9 23.6 - - + -
359B ILE* 4.0 13.2 - - + -
361B ILE* 3.8 32.5 - - + +
394B MET* 3.6 38.1 - - + -
395B GLY 2.9 7.6 + - - +
397B VAL* 1.3 80.7 - - - +
399B MET* 1.3 69.0 + - + +
401B GLY* 3.0 6.2 + - - -
402B PHE* 3.0 29.4 - - + -
415B PHE* 4.7 4.9 - - + -
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Residues in contact with MET 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B LEU* 4.0 20.0 - - + +
215B LEU* 3.8 27.2 + - + +
288B VAL* 3.9 15.7 - - + -
289B ASP 4.0 3.8 - - - +
290B SER* 3.6 35.0 - - - -
394B MET 4.1 5.8 - - - +
395B GLY 3.0 13.9 + - - +
396B ALA 4.1 1.3 - - - +
398B ILE* 1.3 81.2 - - + +
400B GLU* 1.3 57.8 + - - +
401B GLY 3.0 0.2 - - - -
402B PHE* 2.7 29.1 + - - +
404B VAL* 4.1 21.3 - - + -
406B PHE* 3.8 31.9 - - + -
415B PHE* 6.2 0.2 - - + -
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Residues in contact with GLU 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B SER* 3.3 25.8 + - - -
75B TYR* 2.5 26.7 + - - +
215B LEU* 3.2 30.7 - - + +
217B GLY* 3.6 24.7 + - - +
364B GLN 5.7 0.5 - - - +
365B GLN* 4.7 17.5 + - + +
396B ALA* 2.8 30.5 + - + +
397B VAL* 4.4 4.9 - - - +
399B MET* 1.3 71.8 - - - +
401B GLY* 1.3 59.2 + - - +
402B PHE 3.8 0.4 + - - -
418B SER* 4.2 3.9 + - - -
420B CYS 4.7 1.0 - - - +
421B HIS* 3.5 18.0 - - - +
422B VAL 5.1 0.2 + - - -
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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
------------------------------------------------------------
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