Contacts of the helix formed by residues 267 - 275 (chain C) in PDB entry 5DWQ
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 267 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C ARG* 3.4 53.1 + - - +
264C PHE 3.1 13.1 + - - -
265C ASN 3.2 0.4 - - - -
266C GLU* 1.3 77.7 - - - +
268C MET* 1.3 62.1 + - - +
269C LEU* 3.2 4.9 - - - +
270C GLU* 2.7 60.3 + - - +
271C SER* 3.9 2.4 + - - -
368C HIS* 3.5 18.4 + - - -
442C ALA* 3.5 15.3 + - - +
443C ASN 2.6 35.1 + - - -
444C LYS* 5.5 0.6 - - - +
446C GLN* 3.8 6.9 - - - +
447C SER 3.6 30.1 - - - +
448C TYR* 3.9 15.3 - - + -
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Residues in contact with MET 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C TYR* 4.1 13.9 - - - +
191C VAL* 3.2 38.1 - - + +
192C GLY* 3.9 1.6 - - - -
256C SER* 3.5 13.5 - - - +
257C GLU 4.0 3.6 - - - +
258C PRO* 3.7 28.1 + - + +
264C PHE 4.9 0.2 + - - -
265C ASN 4.6 0.6 + - - -
266C GLU* 3.1 10.9 - - + +
267C ARG* 1.3 75.4 - - - +
269C LEU* 1.3 59.0 + - - +
270C GLU 3.2 0.4 - - - -
271C SER* 3.1 11.7 + - - -
272C TYR* 2.9 26.3 + - - +
501C SFG 3.2 61.5 - - + +
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Residues in contact with LEU 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258C PRO* 3.6 34.9 + - + +
259C MET* 5.0 1.3 - - + +
263C LEU* 3.9 26.5 - - + +
264C PHE* 3.5 39.7 - - + +
267C ARG* 3.2 2.2 - - - -
268C MET* 1.3 79.2 - - - +
270C GLU* 1.3 57.4 + - - +
272C TYR* 3.2 7.6 + - + +
273C LEU* 2.8 34.4 + - + +
359C PHE* 3.6 35.7 - - + -
367C LEU* 3.5 17.0 - - + -
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Residues in contact with GLU 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C ARG* 3.8 19.2 - - - +
267C ARG* 2.7 63.5 + - - +
268C MET 3.2 0.4 - - - -
269C LEU* 1.3 78.1 - - - +
271C SER* 1.3 56.6 + - - +
274C HIS* 2.8 29.3 + - - +
364C GLU* 3.6 36.0 - - + +
367C LEU* 3.9 18.1 - - + +
368C HIS* 3.3 18.6 + - - -
448C TYR* 3.4 16.3 + - - -
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Residues in contact with SER 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C PHE* 4.4 2.6 - - - -
140C ARG* 3.2 9.6 + - - +
191C VAL* 4.6 3.4 - - - -
242C VAL* 3.7 13.5 - - - +
243C GLU* 2.6 28.2 + - - -
267C ARG 4.2 3.1 + - - -
268C MET* 3.1 20.3 + - - -
270C GLU* 1.3 75.5 - - - +
272C TYR* 1.3 65.0 + - - +
274C HIS* 3.4 4.6 + - - +
275C ALA* 3.1 23.2 + - - +
501C SFG 3.3 21.3 + - - -
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Residues in contact with TYR 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C VAL* 4.5 9.6 - - + +
254C ILE* 3.7 26.0 - - + +
256C SER* 3.4 28.9 - - - +
258C PRO* 3.8 20.0 - - + -
268C MET 2.9 13.6 + - - +
269C LEU* 3.3 15.5 - - + +
271C SER* 1.3 77.6 - - - +
273C LEU* 1.3 62.2 + - + +
275C ALA* 3.5 14.2 + - - +
276C LYS 4.1 1.2 + - - -
285C MET* 3.4 30.0 - - + +
286C PHE 2.9 21.5 + - - -
287C PRO* 2.6 40.8 + - + -
359C PHE* 3.9 21.5 - + - -
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Residues in contact with LEU 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269C LEU 2.8 17.4 + - - +
270C GLU 4.0 3.4 - - - +
272C TYR* 1.3 71.1 - - + +
274C HIS* 1.3 65.5 + - - +
275C ALA 3.1 0.2 - - - -
276C LYS* 3.1 28.3 + - - +
285C MET* 4.4 1.8 - - + -
357C VAL* 5.4 0.2 - - + -
359C PHE* 3.4 52.5 - - + +
362C ALA* 3.6 21.5 - - + +
363C LYS 4.0 8.7 - - - +
364C GLU* 3.9 27.6 - - - +
367C LEU* 3.6 33.0 - - + -
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Residues in contact with HIS 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C VAL* 3.6 32.3 - - + +
242C VAL 4.2 4.9 - - - -
243C GLU* 3.6 32.1 + - + +
270C GLU 2.8 20.1 + - - +
271C SER* 3.4 11.0 - - - +
273C LEU* 1.3 77.1 - - - +
275C ALA* 1.3 58.3 + - - +
276C LYS 3.1 5.6 + - - -
277C LYS* 3.4 47.9 + - + +
364C GLU* 2.7 31.0 + - - +
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Residues in contact with ALA 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C LEU* 3.9 8.7 - - + -
191C VAL* 3.8 24.5 - - + -
242C VAL* 4.0 10.8 - - + -
254C ILE* 3.2 18.7 - - + +
271C SER 3.1 12.8 + - - +
272C TYR 3.6 11.9 - - - +
273C LEU 3.1 0.8 - - - -
274C HIS* 1.3 72.6 - - - +
276C LYS* 1.3 56.2 + - - +
277C LYS 3.1 6.3 - - - -
278C TYR* 3.1 30.4 + - - +
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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