Contacts of the helix formed by residues 295 - 299 (chain B) in PDB entry 2WFD
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 ARG 295 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A MSE 3.7 33.2 - - + -
260A GLY 2.9 29.3 + - - +
261A PRO* 4.6 1.3 - - + -
293B THR* 3.3 6.4 + - - -
294B LEU* 1.3 86.5 - - - +
296B PRO* 1.3 62.1 - - - +
297B GLU* 2.5 33.6 + - - +
298B THR* 2.7 37.2 + - + +
299B MSE 3.8 4.7 - - - +
395B ASP* 5.9 4.8 + - - +
432B ILE* 3.9 10.1 - - - +
467B ILE 4.4 1.8 + - - -
468B TYR* 3.3 32.0 + - - +
471B GLY* 3.7 8.9 + - - -
472B PHE* 3.6 24.2 - - + +
487B VAL* 3.3 22.2 - - - +
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Residues in contact with PRO 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B THR* 4.1 18.8 - - + +
293B THR* 3.8 7.4 - - + -
294B LEU 3.5 8.5 - - - +
295B ARG* 1.3 85.7 - - - +
297B GLU* 1.3 70.9 - - - +
298B THR 3.1 0.4 - - - -
299B MSE 3.2 28.3 + - + +
366B LEU* 4.1 1.4 - - - +
491B LYS* 3.8 31.9 - - + +
494B ILE* 3.4 15.3 - - + +
495B GLN* 4.4 8.1 - - + +
498B MSE 3.5 23.4 - - + +
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Residues in contact with GLU 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ARG* 2.5 54.1 + - - +
296B PRO* 1.3 90.0 - - - +
298B THR* 1.3 63.9 + - - +
299B MSE 3.2 1.1 + - - -
300B PHE* 3.6 19.2 - - - -
431B VAL* 3.7 9.0 - - - +
432B ILE* 3.9 13.5 - - + -
472B PHE* 5.5 0.2 - - - -
477B MSE 4.1 13.0 - - - +
487B VAL* 3.6 24.7 - - + -
490B VAL* 4.6 1.3 - - + -
491B LYS* 3.8 21.4 - - - +
494B ILE* 3.6 26.4 - - + +
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Residues in contact with THR 298 (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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259A MSE 3.7 13.6 - - - +
295B ARG* 2.7 28.4 + - + +
297B GLU* 1.3 93.3 - - - +
299B MSE 1.3 68.9 + - - +
300B PHE 2.9 12.4 + - - -
301B GLY 3.0 12.3 + - - -
392B VAL* 3.4 23.6 - - - +
395B ASP* 4.5 15.9 - - + -
431B VAL* 4.0 12.7 - - + +
432B ILE* 4.1 15.3 - - + -
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Residues in contact with MSE 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A MSE 3.1 36.1 - - + -
267B LEU* 3.6 38.1 - - + -
293B THR* 3.3 22.0 - - - +
295B ARG 3.8 1.6 - - - +
296B PRO* 3.3 27.1 - - + +
297B GLU 3.2 1.8 - - - -
298B THR* 1.3 86.2 - - - +
300B PHE* 1.3 59.5 + - - +
301B GLY 3.2 1.1 - - - -
302B GLN* 3.5 25.5 - - - +
365B PRO 3.6 4.2 - - - +
366B LEU* 3.6 13.4 - - + +
367B THR 3.6 11.4 + - - -
390B THR* 3.2 25.6 - - + +
392B VAL* 4.2 2.0 - - + -
498B MSE 4.5 2.0 - - + -
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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