Contacts of the strand formed by residues 204 - 217 (chain D) in PDB entry 1C9T
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 LYS 204 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D ILE* 4.2 1.1 - - - -
122D SER* 3.3 27.9 + - - +
123D LEU 3.4 20.0 + - - +
124D PRO* 4.1 20.4 - - + -
125D THR* 5.2 12.0 - - - +
200D VAL* 3.1 9.0 - - - +
201D CYS 3.0 32.8 + - - +
202D SER* 3.8 10.8 - - - +
203D GLY* 1.3 81.8 - - - +
209D LEU* 1.3 59.7 - - - +
210D GLN* 3.3 8.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 209 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D SER* 3.4 25.6 - - - +
47D ILE* 4.7 0.7 - - + -
53D VAL* 3.3 32.3 - - + -
121D ILE* 3.9 16.3 - - + +
122D SER 2.7 19.5 + - - +
123D LEU* 4.2 10.3 - - + -
124D PRO* 3.2 21.9 - - + +
198D PRO* 3.8 21.8 - - + -
199D VAL 4.0 3.4 - - - +
200D VAL* 4.6 2.9 - - + +
204D LYS* 1.3 69.8 - - - +
210D GLN* 1.3 57.5 + - - +
211D GLY 4.1 7.9 - - - +
212D ILE* 5.2 2.7 - - + -
231D VAL* 3.3 30.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 210 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D PRO* 3.2 22.8 - - - +
127D SER 3.4 10.0 - - - +
128D CYS* 3.9 7.7 - - - +
129D ALA* 3.5 31.2 + - + +
162D ILE* 5.0 0.6 - - + +
181D PHE* 3.5 17.3 - - + -
199D VAL 2.8 9.7 + - - -
201D CYS* 3.4 43.2 - - + +
204D LYS* 3.3 7.9 + - - +
209D LEU* 1.3 73.8 - - - +
211D GLY* 1.3 56.7 + - - +
230D LYS* 3.8 1.9 - - - +
231D VAL* 2.9 23.6 + - - +
232D CYS* 4.1 14.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 211 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181D PHE* 3.5 15.7 - - - -
197D GLY 3.9 0.3 - - - +
198D PRO* 3.7 2.4 - - - +
199D VAL* 2.9 34.6 + - - +
209D LEU* 3.7 4.2 - - - +
210D GLN* 1.3 82.2 - - - +
212D ILE* 1.3 66.8 + - - +
228D TYR* 4.4 0.2 - - - -
229D THR 3.0 12.6 - - - -
231D VAL* 3.8 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 212 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D SER* 6.1 0.4 - - - +
53D VAL* 3.9 13.9 - - + -
54D SER* 3.8 11.0 - - - +
55D ALA* 3.6 11.7 - - + +
102D ASP 4.3 6.5 - - - +
103D ILE* 3.8 30.3 - - + -
196D GLY* 3.3 40.8 - - - +
197D GLY 3.3 3.8 - - - +
209D LEU* 5.2 5.2 - - + -
211D GLY* 1.3 75.2 - - - +
213D VAL* 1.3 68.9 + - - +
214D SER 3.1 1.7 + - - -
228D TYR* 3.3 5.4 - - - +
229D THR* 3.0 36.1 + - - +
231D VAL* 3.5 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 213 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D ALA* 4.0 3.6 - - - +
138D ILE* 3.9 18.6 - - + -
139D SER 5.0 1.8 - - - +
190D SER* 3.7 24.7 - - - +
194D ASP* 3.0 37.9 - - + +
195D SER* 3.5 5.7 - - - +
196D GLY 2.9 22.2 + - - -
197D GLY* 3.0 21.5 + - - +
198D PRO 4.5 1.3 - - - +
199D VAL* 4.7 0.2 - - + -
211D GLY 4.3 0.2 + - - -
212D ILE* 1.3 72.7 - - - +
214D SER* 1.3 59.7 + - - +
228D TYR* 3.3 22.1 - - + -
34J LYS* 4.0 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 214 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D HIS* 3.6 6.3 + - - -
99D LEU* 4.6 2.4 + - - +
102D ASP* 2.7 34.6 + - - +
195D SER* 3.5 5.2 + - - -
212D ILE 3.1 8.3 + - - -
213D VAL* 1.3 75.8 - - - +
215D TRP* 1.3 78.3 + - - +
227D VAL 3.3 13.0 + - - -
228D TYR* 4.3 4.0 - - - -
229D THR* 4.0 7.9 - - - -
33J CYS* 3.6 2.3 - - - -
34J LYS* 2.8 29.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 215 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D THR 4.9 4.7 - - - -
99D LEU* 3.6 26.8 + - + +
172D TYR* 3.6 28.0 - + - -
175D GLN* 4.1 21.8 - - + -
176D ILE* 4.0 18.4 - - + -
180D MET* 3.6 29.3 - - + +
214D SER* 1.3 99.3 - - - +
216D GLY* 1.3 70.9 + - - +
227D VAL* 2.8 52.9 + - + +
31J LEU* 3.1 36.8 - - + -
32J HIS 3.3 15.7 - - - +
33J CYS* 3.6 8.7 - - - +
34J LYS* 3.7 14.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 216 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172D TYR* 3.7 13.9 - - - -
189D ASP* 6.0 0.9 - - - -
215D TRP* 1.3 93.7 - - - +
217D SER* 1.3 63.3 + - - -
219D GLY 3.8 5.7 + - - +
225D PRO 4.5 3.1 - - - -
226D GLY* 5.1 0.7 - - - -
227D VAL 4.7 0.2 - - - -
31J LEU* 3.8 1.9 - - - +
32J HIS* 3.0 28.8 + - - +
34J LYS* 4.2 6.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 217 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172D TYR* 3.2 25.9 + - - -
189D ASP* 5.2 0.7 - - - +
216D GLY* 1.3 69.3 - - - -
219D GLY* 1.3 68.1 + - - +
220D CYS* 3.4 2.4 + - - -
221D GLN* 3.9 16.4 - - - +
224D LYS* 3.6 33.2 + - - +
30J ASP* 3.9 20.0 - - - -
31J LEU* 4.4 9.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 219 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189D ASP* 4.5 1.4 - - - +
192D GLN* 4.4 11.6 + - - +
216D GLY 3.8 5.9 + - - +
217D SER* 1.3 75.7 + - - +
220D CYS* 1.3 74.1 + - - -
221D GLN* 4.0 8.5 - - - -
30J ASP* 3.4 20.3 + - - +
32J HIS* 5.7 1.9 - - - +
34J LYS* 4.4 7.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 220 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D VAL* 3.4 15.0 - - + -
146D SER* 4.0 20.4 + - - +
189D ASP* 3.9 4.3 - - - -
190D SER 3.7 3.8 - - - +
191D CYS* 2.0 57.2 - - + -
192D GLN* 3.7 11.4 - - - -
217D SER 3.4 0.6 + - - -
219D GLY* 1.3 83.4 - - - -
221D GLN* 1.3 91.9 + - - +
34J LYS* 5.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 221 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D VAL* 3.5 26.0 - - + -
146D SER* 4.9 3.6 - - - -
187D GLY* 3.1 5.1 - - - -
188D GLY* 3.0 44.2 + - - +
189D ASP* 3.2 29.5 + - + +
220D CYS* 1.3 71.7 - - - +
221D GLN* 1.3 64.6 + - - +
222D LYS 3.5 0.9 + - - -
224D LYS 5.2 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 221 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D SER* 4.9 11.8 - - - -
147D SER* 5.6 1.7 + - - -
184D TYR 5.0 1.7 - - - +
187D GLY* 4.4 3.2 - - - -
217D SER* 3.9 16.6 - - - +
219D GLY* 4.0 6.1 - - - -
220D CYS* 2.9 38.2 + - - +
221D ALA* 1.3 80.6 - - - +
222D LYS* 1.3 68.7 + - - +
223D ASN 3.5 0.5 + - - -
224D LYS* 3.2 33.1 + - + +
----------------------------------------------------------
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