Contacts of the helix formed by residues 248 - 260 (chain B) in PDB entry 3COG
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 SER 248 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A SER* 3.5 25.2 - - - +
251A ASP* 2.9 36.4 + - - -
246B VAL 3.9 1.4 + - - -
247B PRO* 1.3 73.9 - - - +
249B PRO* 1.4 71.2 - - - +
250B ILE* 3.0 19.6 + - - +
251B ASP* 3.2 12.0 + - - +
252B CYS* 3.0 20.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A ASP 6.0 1.8 - - - +
221A VAL* 6.2 4.7 - - + +
251A ASP* 4.8 3.1 - - - +
41B ILE* 4.0 3.5 - - + +
42B SER 3.4 27.1 - - - +
43B LEU* 4.0 19.7 - - + +
61B SER* 4.5 10.1 - - - +
65B ASN* 4.0 24.0 - - - +
67B THR* 3.3 17.9 - - - +
68B ARG* 5.7 0.2 - - + -
247B PRO 3.5 4.7 - - - +
248B SER* 1.4 87.4 - - - +
250B ILE* 1.3 55.2 + - - +
252B CYS* 3.4 8.4 + - + -
253B TYR* 3.0 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 250 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A ILE* 3.3 51.4 - - + -
251A ASP* 4.2 5.2 - - - +
254A LEU* 4.4 5.6 - - + -
41B ILE* 4.0 20.9 - - + -
43B LEU* 3.6 28.9 - - + -
248B SER* 3.0 9.7 + - - +
249B PRO* 1.3 72.7 - - - +
251B ASP* 1.3 61.3 + - - +
253B TYR* 3.2 5.6 + - + +
254B LEU* 3.0 41.1 + - + +
250C ILE* 6.4 1.6 - - + -
41D ILE* 5.8 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU* 5.3 2.9 - - - +
248A SER* 2.9 41.3 + - - -
249A PRO* 4.8 3.0 - - - +
250A ILE* 4.5 3.3 - - - +
219B ASP 4.8 3.1 - - - +
220B VAL* 4.1 18.5 - - + +
221B VAL 4.2 12.1 + - - +
222B MET* 3.5 16.2 - - + +
247B PRO* 4.9 1.3 - - + +
248B SER* 3.2 14.1 + - - +
250B ILE* 1.3 76.1 - - - +
252B CYS* 1.3 60.0 + - - +
254B LEU* 3.3 15.9 + - - +
255B CYS* 2.8 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 252 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B THR* 3.9 13.0 - - + +
68B ARG* 3.7 29.6 - - - -
71B LEU* 3.6 27.4 - - + +
222B MET* 3.7 0.4 - - - -
247B PRO* 3.4 28.9 - - - -
248B SER 3.0 20.3 + - - -
249B PRO* 3.5 9.0 - - - +
251B ASP* 1.3 77.1 - - - +
253B TYR* 1.3 57.2 + - - +
255B CYS 3.4 0.2 + - - -
256B ASN* 2.8 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 253 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B VAL* 3.5 28.0 - - + +
39B PRO* 3.7 15.7 - - + -
41B ILE* 3.6 35.2 - - + -
67B THR* 3.7 12.2 - - + +
249B PRO 3.0 11.7 + - - +
250B ILE* 3.4 8.3 - - + +
252B CYS* 1.3 75.5 - - - +
254B LEU* 1.3 70.4 + - + +
256B ASN* 3.2 8.1 + - + +
257B ARG* 2.9 41.2 + - + +
217C HIS 4.6 0.7 + - - -
219C ASP* 2.6 44.2 + - - +
254C LEU* 4.8 2.5 - - + -
43D LEU* 3.8 20.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 254 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU* 3.8 17.5 - - + -
250A ILE* 6.2 0.2 - - + -
215B ASN* 3.1 7.9 - - - +
219B ASP 4.7 0.4 - - - +
220B VAL* 3.7 23.1 - - + -
250B ILE* 3.0 34.8 + - + +
251B ASP* 3.3 7.8 + - - +
253B TYR* 1.3 82.1 - - + +
255B CYS* 1.3 61.2 + - - +
257B ARG* 3.3 4.2 + - - -
258B GLY 2.9 23.0 + - - -
253C TYR* 3.4 29.8 - - + +
254C LEU* 3.8 26.2 - - + -
257C ARG* 3.2 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LEU* 4.2 12.3 - - + -
210B ALA* 3.9 20.2 - - - -
214B MET 4.6 3.1 - - - +
215B ASN* 3.3 25.5 + - + +
220B VAL* 4.3 4.0 - - + +
222B MET* 3.8 26.9 - - + -
224B LEU* 4.4 7.6 - - - -
251B ASP 2.8 18.1 + - - +
252B CYS 3.8 3.1 - - - +
254B LEU* 1.3 75.4 - - - +
256B ASN* 1.3 65.7 + - - +
258B GLY* 3.1 1.6 + - - -
259B LEU* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 256 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ALA 4.6 2.2 + - - -
27B GLN* 2.9 36.5 + - - +
39B PRO* 5.4 0.7 - - - +
67B THR* 5.0 1.1 - - + +
70B CYS* 3.8 2.6 - - - +
71B LEU* 3.4 33.7 + - + +
74B ALA* 4.1 13.7 - - - +
252B CYS 2.8 19.1 + - - +
253B TYR* 3.6 7.9 - - + +
255B CYS* 1.3 76.9 - - - +
257B ARG* 1.3 61.7 + - - +
259B LEU* 3.4 15.2 + - - +
260B LYS* 3.3 26.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B TYR* 2.9 30.6 + - + +
254B LEU* 3.5 6.3 - - - +
255B CYS 3.1 0.2 - - - -
256B ASN* 1.3 74.3 - - - +
258B GLY* 1.3 67.5 + - - +
260B LYS* 3.2 26.0 + - - +
261B THR 4.2 0.5 + - - -
215C ASN* 2.9 25.3 + - - +
217C HIS* 3.4 43.9 + - + +
219C ASP* 2.7 41.8 + - - +
254C LEU* 3.2 37.0 + - - +
257C ARG* 3.4 31.0 - - - +
258C GLY* 3.7 8.9 - - - +
344C PHE* 5.1 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 258 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B MET 4.1 0.4 - - - -
215B ASN* 3.6 18.4 - - - -
217B HIS* 3.9 13.0 - - - -
254B LEU 2.9 15.3 + - - -
255B CYS 3.1 3.8 + - - -
257B ARG* 1.3 78.2 - - - +
259B LEU* 1.3 59.3 + - - +
261B THR* 3.1 15.3 + - - -
265B ARG* 2.8 22.5 + - - -
217C HIS* 5.8 0.2 - - - -
257C ARG* 3.7 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 259 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ALA* 3.7 16.7 - - - +
71B LEU* 3.9 13.7 - - + -
74B ALA* 4.3 7.6 - - + -
75B VAL* 3.8 25.1 - - + -
78B LEU* 4.1 23.7 - - + +
214B MET* 3.4 48.0 + - + +
255B CYS* 2.9 17.7 + - - +
256B ASN* 3.5 18.6 - - - +
257B ARG 3.2 0.2 - - - -
258B GLY* 1.3 72.2 - - - +
260B LYS* 1.3 59.8 + - - +
261B THR 3.0 7.1 + - - -
262B LEU* 3.1 23.4 + - + +
265B ARG* 4.3 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 260 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ALA* 3.5 21.8 - - - +
23B ILE* 3.6 28.9 + - + +
27B GLN* 2.8 37.9 + - - +
37B VAL 5.7 0.4 + - - -
38B VAL* 4.8 7.9 - - - +
39B PRO* 4.7 4.6 - - - +
256B ASN* 3.3 29.0 - - - +
257B ARG* 3.5 14.3 - - - +
258B GLY 3.2 0.8 - - - -
259B LEU* 1.3 76.3 - - - +
261B THR* 1.3 61.4 + - + +
263B HIS* 3.4 18.8 - - - -
344C PHE* 3.7 55.6 - - + +
380C LEU* 4.7 1.0 - - - +
----------------------------------------------------------
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