Contacts of the helix formed by residues 295 - 306 (chain X) in PDB entry 3FEW
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 295 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77X VAL* 6.0 0.4 - - + -
90X VAL* 3.7 15.3 - - + -
91X TYR* 3.4 18.4 - + - -
116X ALA 5.9 0.2 - - - -
119X TRP* 3.6 37.7 - + + +
209X PRO* 3.6 32.5 - - + -
210X PRO* 3.5 32.1 - - + -
215X PHE* 5.6 3.8 - + - -
291X VAL* 3.3 34.3 - - + -
292X PHE* 3.5 2.9 + - - -
293X TYR 3.1 0.8 - - - -
294X SER* 1.3 78.6 - - - +
296X SER* 1.3 65.9 + - - +
297X MET* 4.4 1.1 - - + +
298X ASN* 3.0 38.5 + - - +
299X ARG* 3.1 13.6 + - - +
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Residues in contact with SER 296 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111X PRO* 6.3 0.2 - - - -
119X TRP 5.9 0.8 + - - -
120X ASP* 2.9 37.6 + - - +
121X LYS* 4.5 1.7 + - - +
294X SER 3.8 2.8 + - - -
295X PHE* 1.3 69.3 - - - +
297X MET* 1.3 67.4 + - - +
299X ARG* 3.7 27.2 - - - +
300X ASP* 2.9 41.0 + - - +
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Residues in contact with MET 297 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119X TRP 5.2 0.9 - - - +
120X ASP* 5.5 0.4 - - - +
121X LYS* 4.0 46.2 - - + +
124X LEU* 3.7 24.7 - - - -
144X ASN* 6.3 0.4 - - - -
205X TRP* 3.8 25.6 - - + +
210X PRO* 4.2 20.9 - - + -
211X ASN* 3.2 27.1 - - - +
295X PHE* 3.2 0.6 - - + +
296X SER* 1.3 80.2 + - - +
298X ASN* 1.3 58.8 + - - +
300X ASP* 3.8 6.0 + - - +
301X ARG* 3.3 39.2 + - - +
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Residues in contact with ASN 298 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210X PRO 3.1 27.3 + - - +
211X ASN* 5.6 0.2 - - - +
212X VAL 5.4 0.4 + - - -
213X ARG* 3.7 0.9 + - - -
292X PHE* 2.8 56.9 + - + +
293X TYR* 5.1 1.1 - - - -
295X PHE* 3.0 22.4 + - - +
297X MET* 1.3 79.4 - - - +
299X ARG* 1.3 62.6 + - - +
300X ASP 3.3 0.2 - - - -
301X ARG* 2.8 32.0 + - - +
302X ILE* 3.2 30.0 + - - +
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Residues in contact with ARG 299 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111X PRO* 4.1 24.0 - - - +
293X TYR* 3.0 80.6 + - + +
294X SER* 3.1 24.9 + - - +
295X PHE 3.1 5.8 + - - +
296X SER* 3.2 31.6 + - - +
298X ASN* 1.3 75.2 - - - +
300X ASP* 1.3 62.9 + - - +
302X ILE* 3.3 6.8 + - - +
303X GLN* 2.9 27.5 + - - +
307X LEU* 6.1 0.2 - - - +
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Residues in contact with ASP 300 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296X SER* 2.9 29.8 + - - +
297X MET* 4.0 6.3 - - - +
299X ARG* 1.3 78.1 - - - +
301X ARG* 1.3 66.2 + - - +
303X GLN* 3.1 8.5 + - - +
304X SER* 3.0 28.3 + - - +
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Residues in contact with ARG 301 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211X ASN* 5.4 0.8 + - - -
213X ARG* 2.9 22.9 - - - +
230X ASP* 2.9 37.8 + - - +
231X TYR* 3.7 21.8 - - + -
297X MET* 3.3 30.2 + - - +
298X ASN* 2.8 37.1 + - - +
299X ARG 3.4 0.8 - - - -
300X ASP* 1.3 77.5 - - - +
302X ILE* 1.3 57.8 + - - +
304X SER* 3.5 3.3 + - - +
305X ASP* 2.9 44.8 + - - +
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Residues in contact with ILE 302 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230X ASP 4.6 1.6 - - - +
231X TYR* 3.8 38.1 - - + +
289X TYR* 5.0 4.0 - - + +
292X PHE* 3.9 18.4 - - + -
293X TYR* 4.4 22.0 - - + -
298X ASN 3.2 18.2 + - - +
299X ARG* 3.6 6.5 - - - +
301X ARG* 1.3 75.2 - - - +
303X GLN* 1.3 56.9 + - - +
306X VAL* 3.0 35.3 + - + -
307X LEU* 3.2 16.6 + - + +
443X ALA* 4.0 26.9 - - + -
444X VAL* 5.7 1.1 - - + -
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Residues in contact with GLN 303 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299X ARG 2.9 17.0 + - - +
300X ASP* 3.1 11.2 + - - +
302X ILE* 1.3 78.0 - - - +
304X SER* 1.3 61.5 + - - +
307X LEU* 3.5 22.0 + - - +
308X ASN* 2.9 60.0 + - - +
341X LYS* 3.0 30.0 + - - +
342X ASN* 5.4 0.8 - - - +
344X GLN* 5.2 7.9 - - - +
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Residues in contact with SER 304 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300X ASP* 3.0 16.4 + - - +
301X ARG* 4.0 3.1 - - - -
303X GLN* 1.3 79.0 - - - +
305X ASP* 1.3 70.5 + - - +
308X ASN* 3.7 17.6 + - - +
309X LYS* 3.6 22.9 - - - +
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Residues in contact with ASP 305 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231X TYR* 2.5 35.9 + - + +
301X ARG* 2.9 25.4 + - - +
304X SER* 1.3 88.3 - - - +
306X VAL* 1.3 60.1 + - - +
309X LYS* 3.4 11.3 - - - +
397X SER* 2.5 43.5 + - - +
398X LYS* 4.6 6.1 + - - +
400X PHE* 3.6 5.2 - - - -
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Residues in contact with VAL 306 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231X TYR* 3.9 17.7 - - + -
302X ILE* 3.0 21.2 + - + +
304X SER 3.5 0.2 - - - -
305X ASP* 1.3 86.0 - - - +
307X LEU* 1.3 62.3 + - + +
308X ASN 3.4 1.3 - - - -
309X LYS* 3.4 3.0 + - - +
310X ALA* 3.0 29.1 + - - +
399X ALA* 3.7 21.1 - - + -
400X PHE* 4.6 9.0 - - + -
443X ALA* 3.4 34.8 - - + +
444X VAL* 3.9 15.0 - - + -
447X GLY* 4.4 8.7 - - - -
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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