Contacts of the helix formed by residues 280 - 288 (chain A) in PDB entry 3HFV
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 LEU 280 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A HIS* 4.7 3.4 - - + -
50A LEU* 3.8 31.4 - - + +
53A ILE* 3.8 27.3 - - + +
54A LYS* 4.9 4.0 - - + +
138A VAL* 3.9 26.7 - - + -
156A HIS* 2.8 40.0 + - + +
157A GLN 4.2 2.0 - - - -
158A LEU* 4.2 13.7 - - + +
278A LEU* 3.5 25.1 - - + -
279A GLY* 1.3 72.1 - - - -
281A GLU* 1.3 57.8 + - - +
283A LEU* 3.3 4.3 + - + +
284A ALA* 2.8 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LEU* 3.6 15.3 - - + +
154A ILE 4.1 1.8 - - - +
155A PHE* 2.9 17.8 - - + +
156A HIS* 2.7 58.0 + - - +
279A GLY 4.5 0.3 - - - -
280A LEU* 1.3 73.0 + - - +
282A ARG* 1.3 57.3 + - - +
284A ALA* 3.0 1.8 + - - +
285A MET* 2.8 41.4 + - - +
293A ILE* 4.0 24.0 - - + -
296A PHE* 3.7 32.0 - - + +
297A TRP* 5.3 3.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A GLN* 3.4 32.0 + - - +
250A LEU* 3.8 30.6 - - - +
251A GLU* 2.6 59.7 + - - +
252A VAL* 3.7 15.7 - - + -
279A GLY* 3.5 15.2 + - - +
280A LEU 3.2 0.2 - - - -
281A GLU* 1.3 81.5 - - - +
283A LEU* 1.3 59.7 + - - +
285A MET* 3.7 9.0 + - - +
286A ILE* 3.2 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ILE* 4.5 22.9 - - + -
57A VAL* 5.9 0.2 - - + -
215A MET* 4.2 17.0 - - + -
218A LEU* 4.8 8.3 - - + -
219A PHE* 3.8 30.5 - - + -
243A ILE* 4.1 5.6 - - + -
252A VAL* 3.9 28.3 - - + -
278A LEU* 3.9 30.7 - - + -
279A GLY 3.1 13.1 + - - +
280A LEU* 3.6 3.8 - - + +
282A ARG* 1.3 76.3 - - - +
284A ALA* 1.3 59.9 + - - +
286A ILE* 3.2 5.2 + - + +
287A LEU* 2.8 31.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A PRO* 4.9 1.8 - - + -
50A LEU* 4.1 7.6 - - + -
53A ILE* 4.3 14.7 - - + +
280A LEU 2.8 21.5 + - - +
281A GLU 3.0 4.5 + - - +
283A LEU* 1.3 72.0 - - - +
285A MET* 1.3 57.9 + - - +
287A LEU* 4.4 0.4 - - - -
288A TYR* 2.8 52.4 + - + +
290A ILE* 4.3 2.0 - - - -
296A PHE* 3.6 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A SER 3.7 8.5 - - - +
150A GLN* 4.7 15.5 - - + +
245A PHE* 4.0 7.0 - - - -
281A GLU* 2.8 28.0 + - - +
282A ARG* 4.0 9.4 - - - +
284A ALA* 1.3 72.1 - - - +
286A ILE* 1.3 59.7 + - + +
289A ASP* 3.0 20.8 + - - -
290A ILE* 3.0 44.3 + - + +
291A PRO 3.6 13.2 - - - +
292A ASP 3.9 0.2 - - - -
293A ILE* 3.6 40.8 - - - +
296A PHE* 3.9 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A PHE* 4.0 16.8 - - + -
243A ILE* 4.3 20.6 - - + -
245A PHE* 3.2 54.4 - - + -
250A LEU* 4.3 24.9 - - + -
252A VAL* 3.7 25.8 - - + -
282A ARG* 3.2 20.0 - - + +
283A LEU* 3.2 6.0 + - - +
284A ALA 3.1 0.6 - - - -
285A MET* 1.3 80.9 - - + +
287A LEU* 1.3 64.8 + - - +
288A TYR 3.2 1.1 + - - -
289A ASP* 3.6 3.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ILE* 3.3 30.3 - - + -
56A ARG* 4.4 12.6 - - - +
218A LEU* 3.3 32.3 - - + +
219A PHE* 3.6 33.0 - - + -
283A LEU* 2.8 17.6 + - + +
284A ALA 3.8 2.0 - - - +
286A ILE* 1.3 79.0 - - - +
288A TYR* 1.3 87.0 - - + +
316A VAL 5.5 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A PRO* 4.2 12.6 - - + -
52A LEU* 3.1 29.7 - - + +
53A ILE* 4.0 13.1 - - + +
56A ARG* 4.8 6.9 + - - -
284A ALA* 2.8 26.0 + - + +
287A LEU* 1.3 109.4 - - + +
289A ASP* 1.3 73.7 + - - +
290A ILE* 3.8 18.8 - - + -
307A PHE* 3.8 17.9 - + + -
316A VAL* 3.0 41.7 - - + +
318A PHE* 3.0 31.5 + - + +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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