Contacts of the helix formed by residues 394 - 401 (chain B) in PDB entry 4WMJ
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 PHE 394 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356A GLN* 3.7 30.3 - - - +
360A MET* 3.8 31.4 - - + -
361A GLU 4.9 1.3 - - - +
340B ALA* 5.7 0.4 - - + -
342B LEU* 3.8 23.8 - - + -
383B TRP* 3.4 32.1 - + - -
385B GLU* 3.9 16.2 - - + -
390B GLY* 3.0 26.1 + - - -
393B ALA* 1.3 83.8 - - + +
395B TYR* 1.3 90.3 + + - +
396B GLN 3.2 3.8 - - - -
397B LEU* 3.0 17.0 + - - +
398B VAL* 3.4 12.8 + - + +
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Residues in contact with TYR 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A GLU* 5.9 0.2 + - - -
517A GLY 5.1 0.4 - - - -
518A VAL* 5.4 2.2 - - + -
342B LEU* 3.6 26.3 - - + +
344B TYR* 2.8 40.7 + - - -
385B GLU 5.2 0.2 + - - -
387B GLY* 4.8 2.3 - - - -
390B GLY* 3.3 14.2 + - - -
391B GLN* 3.4 44.3 + - + +
394B PHE* 1.3 97.7 - + - +
396B GLN* 1.3 65.9 + - - +
398B VAL* 3.0 12.8 + - + -
399B HIS* 2.9 37.7 + + + +
409B PHE* 3.7 10.8 - + - -
435B GLN* 3.2 26.5 - - + -
439B LEU* 5.9 1.8 - - + -
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Residues in contact with GLN 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A MET 4.2 0.2 - - - +
361A GLU* 3.5 46.6 + - + +
364A GLY 3.0 23.8 + - - +
365A LYS* 3.3 18.9 - - - +
515A GLN* 3.2 16.1 - - - +
516A TRP 4.8 0.4 - - - +
517A GLY* 2.8 33.5 + - - -
518A VAL* 3.9 10.8 + - + +
391B GLN 5.0 0.2 + - - -
394B PHE 3.2 0.6 - - - -
395B TYR* 1.3 74.3 - - - +
397B LEU* 1.3 57.0 + - - +
399B HIS* 3.8 0.9 - - - +
400B GLN* 2.9 50.0 + - - +
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Residues in contact with LEU 397 (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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360A MET* 3.6 36.7 + - + +
364A GLY* 3.6 27.4 - - - +
379A GLY* 3.4 27.4 - - - +
380A PRO 3.6 15.9 - - - +
381A VAL* 4.5 4.9 - - + -
394B PHE 3.0 10.7 + - - +
396B GLN* 1.3 76.4 - - - +
398B VAL* 1.3 65.2 + - - +
401B GLY* 2.8 28.3 + - - +
403B ARG* 4.6 13.1 - - + +
405B ILE* 3.7 26.9 - - + -
475B ARG* 3.8 1.6 + - - -
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Residues in contact with VAL 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B LEU* 6.1 0.4 - - + -
383B TRP* 4.6 6.1 - - + -
394B PHE* 3.8 27.8 - - + +
395B TYR* 3.0 18.2 + - + +
397B LEU* 1.3 77.0 - - + +
399B HIS* 1.3 54.1 + - + +
403B ARG 4.7 2.6 - - - +
405B ILE* 4.2 33.9 - - + +
407B CYS* 4.2 23.8 - - - -
439B LEU* 3.9 22.0 - - + -
475B ARG* 2.7 33.2 + - + -
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Residues in contact with HIS 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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517A GLY 3.7 24.3 + - - +
518A VAL* 6.1 0.7 - - - -
521A GLY 5.1 3.8 + - - -
395B TYR* 2.9 33.5 + + + +
396B GLN 3.9 1.8 - - - +
398B VAL* 1.3 74.3 - - + +
400B GLN* 1.4 62.6 - - + +
435B GLN* 2.8 31.8 + - - -
438B ALA* 3.7 18.9 - - + +
439B LEU* 3.5 39.3 - - + +
471B PHE* 3.9 27.5 - + + +
472B LYS* 4.8 9.5 + - - +
473B GLY 5.2 1.0 + - - -
475B ARG* 3.1 22.5 + - - +
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Residues in contact with GLN 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A GLY 3.6 3.8 - - - +
365A LYS* 3.3 14.4 - - - +
366A TYR* 3.2 37.2 - - + -
516A TRP* 3.8 3.3 - - - +
517A GLY* 3.1 25.1 + - - +
396B GLN* 2.9 34.1 + - - +
399B HIS* 1.4 80.6 - - - +
401B GLY* 1.3 65.1 + - - +
468B HIS 3.1 23.5 + - - +
470B VAL 3.0 23.1 + - - +
471B PHE* 3.9 22.2 - - + -
472B LYS* 6.4 1.1 - - - -
475B ARG* 4.0 0.9 - - - +
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Residues in contact with GLY 401 (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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364A GLY* 3.7 20.8 + - - -
365A LYS 3.9 2.5 - - - -
366A TYR* 4.5 4.6 - - - +
378A THR* 4.7 0.7 - - - -
379A GLY 6.1 0.2 - - - -
397B LEU* 2.8 23.4 + - - -
400B GLN* 1.3 83.1 - - - +
402B THR* 1.3 61.3 + - - -
403B ARG 3.3 5.2 - - - -
472B LYS* 5.3 1.9 - - - +
475B ARG* 3.0 21.7 + - - +
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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