Contacts of the helix formed by residues 301 - 310 (chain A) in PDB entry 1GM5
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 VAL 301 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A LEU* 4.0 24.2 - - + +
285A LYS 5.8 0.9 - - - +
286A GLU* 2.5 44.2 - - + +
287A THR* 5.8 4.7 - - + +
300A GLY* 1.3 74.2 - - - +
302A LYS* 1.3 91.0 - - + +
303A ASP* 2.1 1.6 + - - +
304A ALA* 2.1 29.8 + - - -
305A TYR* 3.8 28.3 - - + -
323A ARG* 3.6 7.9 - - - +
324A LEU* 5.6 0.4 - - + -
327A GLU* 5.7 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LEU* 4.3 15.5 - - + +
106A CYS* 6.2 1.6 - - + -
281A CYS* 3.5 23.4 - - - +
282A CYS* 4.5 16.8 - - - +
284A LEU* 5.0 11.1 - - + +
286A GLU* 5.7 7.6 - - - -
300A GLY* 4.8 4.9 - - - -
301A VAL* 1.3 109.9 - - + +
303A ASP* 1.3 77.7 + - - +
305A TYR* 3.3 2.0 + - - -
306A TYR* 2.8 22.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ILE* 5.6 0.9 - - + -
102A ASP 5.7 0.2 - - - +
103A TYR* 4.2 20.9 - - + -
104A LEU* 3.4 34.2 + - - +
299A LEU* 4.3 25.8 - - + +
300A GLY 4.6 4.7 + - - -
301A VAL 2.1 7.1 + - - -
302A LYS* 1.3 88.9 + - - +
304A ALA* 1.3 48.9 + - - +
306A TYR* 2.6 14.4 - - + +
307A GLY* 2.5 33.1 + - - -
316A HIS* 4.0 9.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A LEU* 4.4 9.7 - - + +
300A GLY 4.1 7.9 - - - +
301A VAL* 2.1 32.3 + - - +
303A ASP* 1.3 64.7 - - - +
305A TYR* 1.3 66.7 + - + +
307A GLY* 3.0 11.4 + - - -
308A MET* 3.1 19.3 + - - +
320A ALA* 3.5 28.4 - - - +
323A ARG* 4.3 11.9 - - + -
324A LEU* 4.5 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A LEU* 3.9 36.1 - - + -
144A GLU* 4.5 15.9 + - + +
146A PHE* 4.1 22.6 - + - -
281A CYS* 3.6 17.0 - - - -
284A LEU* 4.6 11.9 - - + -
301A VAL* 3.8 28.0 - - + -
302A LYS* 3.3 4.0 + - - +
304A ALA* 1.3 76.0 - - - +
306A TYR* 1.3 71.1 + - - +
307A GLY 3.2 0.3 + - - -
308A MET* 3.2 14.2 + - - +
309A HIS* 3.4 16.8 + + - +
324A LEU* 3.1 34.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ASP* 3.6 40.8 + - + -
104A LEU* 3.9 35.7 - - + -
253A ARG* 5.6 1.7 + - - -
277A ILE* 3.9 22.2 - - + -
278A PRO* 4.4 15.2 - - + +
281A CYS* 2.9 11.3 - - - -
302A LYS 2.8 17.7 + - - +
303A ASP* 2.6 20.2 - - + +
305A TYR* 1.3 73.7 - - - +
307A GLY* 1.3 58.9 + - - -
309A HIS* 3.0 12.6 + - - +
310A PHE* 3.1 43.3 + + + +
316A HIS* 4.5 7.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ASP 2.5 16.9 + - - -
304A ALA 3.0 7.7 + - - -
306A TYR* 1.3 71.8 - - - +
308A MET* 1.3 60.5 + - - -
309A HIS 2.9 1.9 + - - -
311A PRO* 3.0 28.4 - - - +
316A HIS* 3.6 29.6 + - - -
317A LEU* 4.5 3.7 - - - +
320A ALA* 4.3 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A PHE* 3.1 56.3 - - + -
147A PRO* 3.2 13.7 - - - +
150A TYR* 3.1 32.8 + - - +
304A ALA 3.1 13.7 + - - +
305A TYR 3.2 5.1 + - - +
307A GLY* 1.3 74.0 - - - +
309A HIS* 1.3 57.9 + - - +
317A LEU* 4.7 3.4 - - - +
320A ALA* 4.1 2.5 - - - -
321A ARG* 3.6 47.6 - - + +
324A LEU* 4.0 9.9 - - + -
738A LEU* 4.3 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A LEU 4.4 1.0 + - - -
143A LEU* 3.8 27.1 + - + -
145A PHE 3.4 18.4 + - - -
146A PHE* 4.1 15.1 - + - -
147A PRO* 4.3 3.8 - - + -
150A TYR* 4.6 0.5 - - - -
256A PRO* 3.3 22.3 - - - +
258A TYR* 2.8 34.5 - + - -
273A PHE* 3.8 13.8 - + - -
277A ILE* 4.0 23.5 - - + +
305A TYR* 3.4 15.9 + + - -
306A TYR 3.0 5.5 + - - +
308A MET* 1.3 76.1 - - - +
310A PHE* 1.3 88.9 + + + +
311A PRO* 3.2 11.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ASP* 4.4 7.6 - - - +
253A ARG* 4.2 23.7 + - - +
254A ILE 5.7 1.6 - - - -
255A LEU* 6.4 0.7 - - + -
256A PRO* 4.1 13.9 - - + -
258A TYR* 3.2 17.5 - + - -
270A ARG* 4.6 1.6 - - + -
273A PHE* 4.0 8.7 - - + -
274A GLU* 3.5 51.1 - - + -
277A ILE* 5.1 5.2 - - + -
278A PRO* 6.1 3.4 - - + -
306A TYR* 3.1 44.9 + + + +
307A GLY* 4.0 2.0 - - - -
309A HIS* 1.3 123.3 - + + +
311A PRO* 1.3 63.4 - - - +
316A HIS* 4.3 4.9 + - - -
----------------------------------------------------------
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