Contacts of the helix formed by residues 293 - 305 (chain A) in PDB entry 1EG4
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 293 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ALA* 4.0 11.4 - - + -
254A PHE* 3.6 20.6 - - + -
288A GLU* 3.7 39.3 - - + +
289A PRO 2.9 12.0 + - - +
290A GLN* 3.7 28.7 - - - +
291A SER 3.8 0.6 - - - -
292A MET* 1.3 75.8 - - - +
294A TRP* 1.3 63.2 + - - +
295A LEU 3.1 1.1 + - - -
296A PRO* 3.3 9.0 - - - +
297A VAL* 3.2 32.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ALA* 4.4 9.9 - - - +
108A THR* 3.9 19.5 - - + -
109A ALA* 4.0 4.8 - - - +
112A LEU* 3.4 27.8 - - + -
205A SER* 4.2 12.6 - - - -
206A LEU* 4.7 4.9 - - + -
241A SER* 3.6 30.9 + - - -
244A ILE* 4.0 24.9 - - + -
245A PRO* 3.5 27.8 - - + +
254A PHE* 3.8 23.1 - + + -
291A SER 3.3 25.0 + - - -
292A MET* 3.8 11.9 - - + +
293A VAL* 1.3 80.2 - - - +
295A LEU* 1.3 100.0 + - + +
297A VAL 3.8 0.2 - - - -
298A LEU* 2.9 30.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A SER* 3.7 33.4 - - - +
211A LEU* 4.0 6.5 - - + -
214A LYS* 3.8 21.1 - - + +
215A TYR* 3.8 27.8 - - + -
218A LEU* 5.2 4.7 - - + -
292A MET* 3.1 22.3 + - + +
294A TRP* 1.3 99.3 - - + +
296A PRO* 1.3 74.3 - - + +
298A LEU* 3.1 23.7 + - + +
299A HIS* 3.2 21.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A LEU* 3.8 26.9 - - + -
215A TYR* 3.5 15.2 - - + +
285A MET* 5.3 2.2 - - + +
288A GLU* 4.0 31.9 - - + +
292A MET 3.3 9.0 - - - +
293A VAL* 3.3 21.8 - - - +
295A LEU* 1.3 94.9 - - + +
297A VAL* 1.3 54.0 + - - +
299A HIS* 3.1 7.3 + - + +
300A ARG* 3.0 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ALA* 3.4 38.1 - - + +
106A TYR* 3.6 34.3 - - + -
109A ALA* 3.5 6.1 - - + -
288A GLU* 4.5 0.2 - - - +
293A VAL* 3.2 26.9 + - + +
294A TRP 4.0 0.7 - - - +
295A LEU 3.1 0.8 - - - -
296A PRO* 1.3 72.0 - - - +
298A LEU* 1.4 60.7 + - - +
300A ARG* 3.0 32.8 + - - +
301A VAL* 2.7 28.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ALA* 3.4 30.6 - - + +
112A LEU* 4.3 10.8 - - + -
113A ARG* 3.8 26.2 - - + +
116A GLN* 4.3 19.1 - - - +
205A SER 4.3 10.8 - - - +
206A LEU* 4.3 15.7 - - + -
214A LYS* 4.9 2.0 - - - +
294A TRP* 2.9 16.4 + - + +
295A LEU* 3.2 27.1 - - + +
297A VAL* 1.4 79.2 - - - +
299A HIS* 1.3 63.4 + - + +
301A VAL* 3.4 1.4 + - - +
302A ALA* 2.9 26.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 299 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A CYS 5.2 0.9 - - - -
208A LYS* 5.2 0.9 - - - -
209A ALA 3.0 28.3 - - - -
210A HIS* 4.4 1.6 - - - -
211A LEU* 3.4 38.6 + - + +
214A LYS* 2.8 28.9 + - - -
295A LEU* 3.2 20.4 + - + +
296A PRO* 3.1 11.2 + - + +
298A LEU* 1.3 82.7 - - + +
300A ARG* 1.3 60.3 + - + +
302A ALA* 3.3 6.6 + - - +
303A ALA* 2.9 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A TYR* 3.0 35.8 + - + -
288A GLU* 2.6 32.7 + - - -
296A PRO* 3.0 17.8 + - - +
297A VAL* 3.0 32.7 + - + +
299A HIS* 1.3 74.6 - - + +
301A VAL* 1.3 65.3 + - - +
303A ALA* 3.4 6.7 + - - +
304A ALA* 3.1 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A TYR* 4.5 7.4 - - + +
109A ALA* 3.7 20.2 - - + +
110A MET* 3.9 31.0 - - + -
113A ARG* 4.1 19.7 - - + -
297A VAL* 2.7 28.5 + - + +
298A LEU* 3.6 6.3 - - - +
300A ARG* 1.3 72.3 - - - +
302A ALA* 1.3 65.8 + - - +
304A ALA* 3.2 15.8 + - - +
305A GLU 3.5 6.8 + - - -
306A THR* 3.8 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ARG* 3.5 41.7 + - - +
298A LEU* 2.9 18.4 + - + +
299A HIS* 3.7 6.7 - - - +
301A VAL* 1.3 76.4 - - - +
303A ALA* 1.3 63.5 + - - +
305A GLU* 3.2 21.1 + - - +
306A THR 4.4 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A HIS 2.9 18.7 + - - +
300A ARG* 3.9 7.2 - - - +
301A VAL 3.2 0.4 - - - -
302A ALA* 1.3 76.9 - - - +
304A ALA* 1.3 59.3 + - - +
305A GLU* 3.1 9.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
300A ARG 3.1 16.8 + - - +
301A VAL* 3.2 8.7 + - - +
303A ALA* 1.3 74.2 - - - +
305A GLU* 1.3 65.4 + - - +
306A THR 3.8 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ARG* 3.8 7.8 + - - -
301A VAL 3.5 0.8 + - - -
302A ALA 3.2 15.3 + - - +
303A ALA 3.1 6.5 - - - +
304A ALA* 1.3 83.1 - - - +
306A THR* 1.3 72.1 + - - +
----------------------------------------------------------
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