Contacts of the helix formed by residues 197 - 207 (chain A) in PDB entry 4C02
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 PRO 197 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A LEU* 4.3 12.1 - - + +
190A SER 5.7 2.5 - - - +
195A GLY 3.8 1.3 - - - +
196A LEU* 1.3 95.7 - - + +
198A PHE* 1.3 68.3 + - + +
199A LEU 3.4 0.9 - - - -
200A VAL* 3.0 27.9 + - + +
201A GLN 3.2 7.4 + - - -
38B ASP* 4.2 1.3 - - - +
43B ARG* 3.3 55.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A SER* 3.6 34.3 - - - -
193A GLY* 4.8 0.9 - - - -
196A LEU 4.0 2.9 - - - -
197A PRO* 1.3 73.0 - - + +
199A LEU* 1.3 62.6 + - + +
201A GLN* 3.3 36.0 + - - +
202A ARG* 4.2 2.1 + - - +
253A ASN* 3.5 38.4 - - - -
37B PHE* 3.1 29.8 - - + -
38B ASP* 3.6 16.7 + - + +
83B TYR* 4.6 5.9 + - - -
88B HIS* 5.0 9.5 + + + -
90B GLY 5.3 0.7 - - - -
91B VAL* 3.6 42.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A PHE* 1.3 75.8 - - + +
200A VAL* 1.3 61.8 + - - +
201A GLN 3.3 0.7 + - - -
202A ARG* 3.5 13.9 + - - +
203A THR* 3.7 11.3 + - - -
27B TYR* 3.3 39.5 - - + +
37B PHE* 4.7 9.0 - - + -
38B ASP* 3.0 11.3 + - - +
47B PHE* 4.0 18.4 - - + -
55B GLU 4.8 0.5 - - - +
56B VAL* 4.2 12.9 - - + +
57B ILE* 5.1 4.5 - - + -
60B PHE* 3.9 28.7 - - + -
83B TYR* 3.9 23.8 - - + +
100B PHE* 4.0 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A LEU* 5.0 8.7 - - + -
196A LEU* 4.1 20.2 - - + -
197A PRO* 3.0 34.0 + - + +
199A LEU* 1.3 76.3 - - - +
201A GLN* 1.3 62.8 + - - +
202A ARG 3.3 0.2 - - - -
203A THR* 3.1 7.6 + - - -
204A VAL* 3.0 36.5 + - + +
27B TYR* 4.7 0.2 - - - +
43B ARG* 4.0 10.1 - - - +
47B PHE* 3.8 24.2 - - + -
1110B EDO 4.4 17.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A GLY 4.8 0.4 - - - +
196A LEU* 3.0 28.5 + - + +
197A PRO 3.2 10.6 + - - +
198A PHE* 3.5 18.4 - - - +
199A LEU 3.2 1.0 - - - -
200A VAL* 1.3 76.1 - - - +
202A ARG* 1.3 56.3 + - - +
204A VAL* 3.6 0.3 + - - -
205A ALA* 3.0 30.4 + - - +
253A ASN* 3.0 23.4 + - - +
265A PHE* 3.8 10.8 - - - -
267A ALA* 3.5 32.0 - - + +
268A SER 3.0 26.4 + - - +
88B HIS* 3.3 21.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A PHE 4.2 0.8 + - - -
199A LEU 3.5 10.8 + - - +
200A VAL 3.3 0.2 - - - -
201A GLN* 1.3 76.0 - - - +
203A THR* 1.3 66.6 + - - +
205A ALA* 3.1 0.9 + - - +
206A ARG* 2.9 69.6 + - - +
268A SER 5.0 0.2 + - - -
269A ASP* 2.7 31.4 + - - +
270A MET* 3.7 21.2 + - - +
1514A EDO 3.9 18.6 + - - -
54B GLN 4.5 2.4 + - - -
55B GLU 3.8 19.3 - - - +
56B VAL* 4.1 8.3 + - - -
57B ILE* 3.7 28.3 - - - +
82B ALA 5.2 2.6 + - - -
83B TYR* 3.8 35.2 - - + +
1108B FLC 5.2 4.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A LEU 3.7 2.6 + - - -
200A VAL* 3.1 11.7 + - - -
202A ARG* 1.3 79.4 - - - +
204A VAL* 1.3 63.3 + - - +
206A ARG* 3.3 2.6 + - - +
207A GLN* 3.2 47.6 + - - +
47B PHE* 3.4 23.1 - - - -
48B LYS 4.3 4.9 - - - +
55B GLU* 2.7 38.4 + - + +
1110B EDO 4.0 22.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LEU* 4.3 9.4 - - + -
183A LEU* 4.5 7.2 - - + -
196A LEU* 3.6 31.9 - - + -
200A VAL* 3.0 22.6 + - + +
201A GLN 4.2 2.0 - - - +
203A THR* 1.3 72.4 - - - +
205A ALA* 1.3 68.6 + - - +
207A GLN* 3.0 19.1 + - - +
208A ILE* 3.3 22.0 + - + +
227A TRP* 3.7 37.4 - - + +
232A VAL* 6.3 0.2 - - + -
266A ILE* 4.8 7.2 - - + -
267A ALA* 5.5 2.2 - - + -
282A ILE* 5.6 0.4 - - + -
1110B EDO 4.7 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A GLN 3.0 19.2 + - - +
202A ARG 3.1 3.6 + - - +
204A VAL* 1.3 78.9 - - - +
206A ARG* 1.3 62.6 + - - +
208A ILE* 3.3 18.0 + - - +
269A ASP* 3.5 32.1 - - + +
280A TRP* 3.6 17.1 - - + -
282A ILE* 3.6 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A ARG* 2.9 40.0 + - - +
203A THR 3.9 4.0 - - - +
205A ALA* 1.3 78.9 - - - +
207A GLN* 1.3 59.9 + - - +
208A ILE 3.3 5.3 + - - +
269A ASP* 2.9 19.0 + - - -
270A MET 3.1 24.9 + - - -
271A THR* 3.8 21.4 + - - +
280A TRP* 6.4 0.4 - - - -
1514A EDO 3.4 37.2 + - - -
53B LYS 4.9 3.8 - - - +
54B GLN* 3.5 31.6 + - + +
55B GLU* 4.6 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A THR* 3.2 24.7 + - - +
204A VAL* 3.0 6.1 + - - +
206A ARG* 1.3 78.2 - - - +
208A ILE* 1.3 61.5 + - - +
209A THR* 3.7 4.7 + - - -
226A SER 4.0 4.3 - - - +
227A TRP* 2.8 42.4 + - + +
228A GLN* 4.0 15.2 + - + +
50B ARG* 3.6 12.7 - - - +
55B GLU* 3.0 34.9 + - - +
1110B EDO 3.8 15.5 + - - -
----------------------------------------------------------
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