Contacts of the helix formed by residues 141 - 155 (chain D) in PDB entry 6Q2J
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 ASP 141 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D ALA 4.1 9.8 + - - +
138D CYS 2.9 14.5 + - - +
139D VAL 4.1 1.1 - - - -
140D GLY* 1.3 76.6 - - - +
142D VAL* 1.3 62.4 + - - +
143D VAL* 3.6 11.7 + - - +
144D CYS* 3.4 21.8 + - + +
145D ASN* 2.9 26.5 + - - +
179D PRO* 4.6 9.3 - - - +
182D ILE* 4.5 14.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 142 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B GLN* 4.5 26.0 - - + -
301B LEU* 6.1 5.4 - - + -
139D VAL 5.2 0.4 - - - -
140D GLY 4.6 7.2 - - - +
141D ASP* 1.3 74.3 + - - +
143D VAL* 1.3 63.8 + - + +
145D ASN* 3.2 9.3 + - + +
146D ALA* 2.9 30.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 143 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141D ASP* 3.4 10.2 + - - +
142D VAL* 1.3 79.6 - - + +
144D CYS* 1.3 58.4 + - - +
146D ALA* 3.4 4.1 + - - +
147D GLN* 3.0 40.6 + - + +
177D ASN 3.7 21.8 - - - +
178D ILE* 5.2 3.6 - - - -
179D PRO* 5.4 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 144 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D CYS* 2.0 60.7 - - - +
141D ASP* 3.4 14.1 + - + +
142D VAL 3.4 0.2 - - - -
143D VAL* 1.3 79.3 - - - +
145D ASN* 1.3 57.3 + - - +
148D LEU* 2.8 31.9 + - - +
174D PHE* 4.0 14.9 - - - -
178D ILE* 4.2 16.6 - - + +
179D PRO* 5.4 1.3 - - + +
182D ILE* 3.7 24.2 - - + -
186D LEU* 5.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 145 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B PRO 6.0 0.2 - - - -
282B MET* 3.4 40.6 - - - +
283B VAL* 3.5 26.2 + - - +
301B LEU* 5.8 1.4 - - - +
138D CYS 3.8 2.2 + - - -
139D VAL* 3.5 29.7 + - - +
141D ASP 2.9 17.9 + - - +
142D VAL* 3.2 11.4 + - + +
144D CYS* 1.3 78.1 - - - +
146D ALA* 1.3 57.5 + - - +
148D LEU* 3.4 4.9 + - - +
149D ALA* 2.9 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 146 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B ASN* 6.5 1.3 - - + -
281B PRO 5.4 5.4 - - - +
142D VAL* 2.9 17.7 + - + +
143D VAL* 4.1 4.5 - - - +
145D ASN* 1.3 73.7 - - - +
147D GLN* 1.3 72.1 + - + +
149D ALA* 3.1 9.2 + - - +
150D SER* 3.0 25.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 147 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D VAL* 3.0 26.6 + - + +
144D CYS 4.2 0.7 - - - +
146D ALA* 1.3 80.2 - - - +
148D LEU* 1.3 57.2 + - - +
150D SER* 3.5 8.3 + - - +
151D TYR* 2.9 28.1 + - - +
173D PHE* 3.3 35.2 - - - +
174D PHE* 3.6 25.5 - - + +
177D ASN* 3.9 34.6 + - + +
178D ILE* 4.3 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 148 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B VAL* 4.1 16.6 - - + -
294B LEU* 4.5 8.1 - - + -
138D CYS* 4.0 12.6 - - + -
139D VAL* 3.7 29.6 - - + -
144D CYS 2.8 19.7 + - - +
145D ASN* 3.6 4.9 - - - +
147D GLN* 1.3 73.9 - - - +
149D ALA* 1.3 60.3 + - - +
151D TYR* 3.3 25.6 - - + +
152D LEU* 2.8 43.8 + - + +
174D PHE* 3.6 18.7 - - + -
186D LEU* 6.1 0.9 - - + -
205D LEU* 4.8 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 149 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B PRO* 3.9 38.4 - - + +
282B MET* 4.8 0.7 - - - -
283B VAL* 3.6 19.0 - - + +
296B THR* 4.5 4.9 - - + +
145D ASN 2.9 14.1 + - - +
146D ALA* 3.1 13.6 + - - +
148D LEU* 1.3 74.0 - - - +
150D SER* 1.3 60.5 + - - +
152D LEU* 3.5 1.0 + - - +
153D LYS* 3.0 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 150 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B PRO* 5.4 3.0 - - - +
146D ALA 3.0 13.0 + - - -
147D GLN* 3.9 13.9 + - - -
149D ALA* 1.3 76.4 - - - +
151D TYR* 1.3 56.6 + - - +
153D LYS* 3.9 12.4 + - - +
154D ALA* 3.0 32.4 + - - +
170D ALA* 4.9 1.3 - - - +
173D PHE* 5.8 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 151 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147D GLN 2.9 20.1 + - - +
148D LEU* 3.3 20.6 - - + +
149D ALA 3.2 0.2 - - - -
150D SER* 1.3 75.3 - - - +
152D LEU* 1.3 79.1 + - + +
154D ALA* 3.2 3.3 + - - -
155D CYS* 2.9 38.3 + - + +
170D ALA* 3.9 25.6 - - + -
171D ILE* 3.5 33.0 - - + +
174D PHE* 3.9 24.5 - + + -
175D TYR* 5.9 1.0 - + - -
204D ALA 4.5 2.2 - - - -
205D LEU 3.3 25.0 + - - -
206D HIS* 3.7 4.2 + - - -
207D SER* 3.1 28.0 + - - -
288D GLN* 5.6 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 152 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B VAL* 3.8 34.8 - - + -
294B LEU* 4.0 26.9 - - + +
296B THR* 3.7 15.3 - - - +
148D LEU* 2.8 28.0 + - + +
149D ALA 4.2 0.2 - - - +
151D TYR* 1.3 87.4 - - + +
153D LYS* 1.3 63.1 + - - +
155D CYS* 3.4 8.8 - - + +
156D SER* 3.2 28.9 + - - -
204D ALA* 3.8 23.8 - - + +
207D SER* 6.1 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 153 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B PRO* 5.0 18.6 - - + +
296B THR* 4.8 10.2 + - + -
298B ASP* 4.8 13.7 - - - +
149D ALA 3.0 19.0 + - - +
150D SER* 4.0 10.9 + - - +
152D LEU* 1.3 79.8 - - - +
154D ALA* 1.3 58.8 + - - +
155D CYS 3.6 0.3 + - - -
156D SER* 4.2 8.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 154 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150D SER 3.0 18.8 + - - +
151D TYR 3.8 2.7 - - - +
153D LYS* 1.3 77.0 - - - +
155D CYS* 1.3 62.7 + - - +
156D SER 3.7 2.2 + - - +
162D CYS* 5.2 2.9 - - - +
163D ASP* 5.0 2.9 + - - +
166D GLN* 4.5 18.7 - - + +
167D CYS* 4.3 9.7 + - - +
170D ALA* 3.8 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 155 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D TYR* 2.9 29.1 + - + +
152D LEU* 3.3 13.0 + - + +
154D ALA* 1.3 78.5 - - - +
156D SER* 1.3 55.9 + - - +
162D CYS* 3.7 14.0 - - - -
167D CYS* 2.0 64.2 - - - -
170D ALA* 4.2 5.8 - - - -
207D SER* 4.6 14.5 - - - -
210D CYS* 4.4 4.0 - - + +
----------------------------------------------------------
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