Contacts of the helix formed by residues 299 - 311 (chain L) in PDB entry 3VD1
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 GLY 299 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136L THR* 5.9 3.3 - - - +
137L ALA 3.0 26.7 - - - -
138L LYS* 3.3 1.6 + - - -
140L ALA* 5.3 0.7 - - - -
143L THR* 4.3 8.3 - - - -
297L CYS 2.3 21.2 + - - -
298L PRO 1.3 69.4 - - - -
300L ARG* 1.3 62.7 + - - +
301L ASP 3.3 1.3 - - - +
302L ARG* 3.5 4.6 + - - +
303L LYS* 3.2 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 300 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137L ALA 4.1 0.4 + - - -
138L LYS* 3.2 38.5 + - + +
296L ALA* 5.0 0.6 - - - +
297L CYS* 3.0 25.3 + - + +
299L GLY* 1.3 76.9 - - - +
301L ASP* 1.3 69.2 + - - +
303L LYS* 3.0 9.4 + - - +
304L ALA* 2.9 28.3 + - + +
703O G 4.0 10.5 + - - -
704O C 4.7 2.0 - - - +
718P T 3.4 39.5 + - - +
719P G 2.6 55.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 301 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152L TYR* 3.6 11.9 - - + -
293L ARG* 2.8 19.5 + - - +
295L CYS* 2.7 37.6 - - - +
296L ALA 4.7 0.2 + - - -
297L CYS 3.3 15.0 + - - +
299L GLY 3.3 0.4 - - - -
300L ARG* 1.3 93.4 + - - +
302L ARG* 1.3 59.1 + - - +
304L ALA* 3.9 6.8 - - - +
305L ASP* 3.0 37.8 + - - +
717P A 6.1 0.2 - - - +
718P T 4.6 10.1 + - - +
719P G 4.8 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 302 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134L SER* 3.9 19.0 + - - -
136L THR* 4.9 7.3 + - - -
143L THR* 3.3 34.4 + - + +
144L TYR 2.7 28.4 + - - -
145L SER* 3.4 11.4 - - - +
146L PRO* 4.9 5.9 - - - +
152L TYR* 3.5 38.8 + - + +
299L GLY* 3.5 10.1 + - - +
300L ARG 3.3 0.4 - - - -
301L ASP* 1.3 77.2 - - - +
303L LYS* 1.3 61.7 + - - +
305L ASP* 4.2 0.5 - - - +
306L GLU* 2.8 76.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 303 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299L GLY 3.2 13.0 + - - +
300L ARG* 3.0 12.5 + - - +
302L ARG* 1.3 77.4 - - - +
304L ALA* 1.3 61.4 + - - +
306L GLU* 3.8 5.3 - - - +
307L ASP* 2.9 71.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 304 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300L ARG* 2.9 17.0 + - + +
301L ASP* 3.4 8.9 + - - +
303L LYS* 1.3 80.7 - - - +
305L ASP* 1.3 64.8 + - - +
307L ASP* 3.9 4.6 - - - +
308L HIS* 3.1 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 305 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148L LEU* 6.6 0.2 - - + -
150L LYS* 2.8 24.9 + - + +
152L TYR* 2.4 34.9 + - - +
293L ARG* 4.6 4.5 + - - -
301L ASP* 3.0 18.8 + - - +
302L ARG 4.2 0.7 - - - +
304L ALA* 1.3 78.1 - - - +
306L GLU* 1.3 58.2 + - - +
308L HIS* 3.9 4.2 + - - +
309L TYR* 2.9 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 306 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145L SER* 2.8 27.1 + - - +
147L LEU* 3.8 23.0 - - + +
302L ARG* 2.8 52.9 + - - +
303L LYS* 3.8 5.2 - - - +
305L ASP* 1.3 76.6 - - - +
307L ASP* 1.3 62.9 + - - +
309L TYR* 3.2 5.4 + - - +
310L ARG* 2.8 61.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 307 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303L LYS* 2.9 53.9 + - - +
304L ALA* 3.9 5.2 - - - +
305L ASP 3.4 0.2 - - - -
306L GLU* 1.3 77.4 - - - +
308L HIS* 1.3 66.2 + - - +
310L ARG* 3.9 11.5 + - - +
311L GLU* 3.1 33.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 308 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304L ALA 3.1 15.0 + - - +
305L ASP* 3.9 4.2 + - - +
307L ASP* 1.3 79.4 - - - +
309L TYR* 1.3 73.6 + - - +
311L GLU* 3.2 18.6 - - - +
312L GLN 3.5 20.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 309 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C ASN* 4.5 9.7 + - - -
147L LEU* 3.9 44.7 + - + +
148L LEU* 4.9 18.8 - - + -
305L ASP 2.9 20.0 + - - +
306L GLU* 3.2 6.3 + - - +
308L HIS* 1.3 86.6 + - - +
310L ARG* 1.3 92.7 + - - +
312L GLN* 3.3 12.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 310 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C ASN* 3.6 46.9 + - + +
222C LEU* 3.9 33.3 - - - +
147L LEU* 3.1 32.9 - - + +
306L GLU* 2.8 44.9 + - - +
307L ASP* 3.9 12.9 + - - +
309L TYR* 1.3 85.0 - - + +
311L GLU* 1.3 58.0 + - + +
312L GLN* 2.6 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 311 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307L ASP* 3.1 19.8 + - + +
308L HIS* 3.2 9.0 - - - +
310L ARG* 1.3 78.3 - - + +
312L GLN* 1.3 77.6 + - - +
----------------------------------------------------------
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