Contacts of the helix formed by residues 136 - 151 (chain D) in PDB entry 4U2M
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 ARG 136 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D PHE* 3.2 1.0 - - - +
135D THR* 1.3 81.1 + - - +
137D HIS* 1.3 65.0 + - - +
138D ALA 3.4 2.2 - - - -
139D SER* 3.4 10.4 + - - +
140D ASP* 3.0 35.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 137 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D LEU* 4.1 5.4 - - + -
45D CYS* 3.8 16.6 - - + -
76D PHE* 3.5 30.9 + + + -
77D MET 2.8 26.4 + - - -
80D ALA* 3.7 29.4 - - + -
134D PHE* 3.2 27.1 + - + +
136D ARG* 1.3 78.8 - - - +
138D ALA* 1.3 59.8 + - - +
140D ASP* 3.1 12.2 + - - +
141D VAL* 2.8 50.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 138 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D SER* 3.6 34.9 - - - +
8D GLN* 3.7 25.6 - - + +
11D LEU* 3.9 19.6 - - + +
80D ALA* 5.0 1.7 - - + +
134D PHE 4.8 0.8 + - - -
135D THR 4.9 3.7 + - - +
136D ARG 3.4 0.6 - - - -
137D HIS* 1.3 77.9 - - - +
139D SER* 1.3 62.4 + - - +
141D VAL* 3.3 6.3 + - - +
142D LEU* 3.1 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 139 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D SER* 3.0 22.3 + - - -
135D THR 5.5 0.4 + - - -
136D ARG* 3.4 12.8 + - - -
137D HIS 3.2 0.6 - - - -
138D ALA* 1.3 75.7 - - - +
140D ASP* 1.3 60.4 + - - +
142D LEU* 3.4 2.0 + - - +
143D LEU* 3.0 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 140 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D ARG* 3.0 33.1 + - - +
137D HIS* 3.1 14.7 + - + +
139D SER* 1.3 77.1 - - - +
141D VAL* 1.3 59.3 + - - +
143D LEU* 3.3 13.3 + - - +
144D ASN* 2.9 42.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 141 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D VAL* 6.3 1.1 - - + -
11D LEU* 4.4 15.5 - - + -
14D LEU* 4.6 7.6 - - + -
41D VAL* 5.0 4.7 - - + -
44D ALA* 3.9 15.9 - - + +
45D CYS* 3.7 16.4 - - - -
77D MET 4.4 2.5 - - - +
137D HIS* 2.8 50.4 + - + +
138D ALA* 3.6 8.5 - - - +
140D ASP* 1.3 75.9 - - - +
142D LEU* 1.3 57.8 + - - +
144D ASN* 3.2 2.4 + - - +
145D LEU* 2.8 45.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 142 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D HIS* 3.8 13.5 - - + -
7D SER* 3.8 18.2 - - - +
10D VAL* 4.1 24.9 - - + -
138D ALA 3.1 13.5 + - - +
139D SER* 3.4 3.8 + - - +
141D VAL* 1.3 76.2 - - - +
143D LEU* 1.3 64.8 + - - +
145D LEU* 3.2 15.3 + - + +
146D ASN 2.9 18.7 + - - -
172D VAL* 5.2 5.2 - - + -
213D MET 3.6 15.7 - - - +
214D TYR* 3.3 30.6 - - - +
215D THR* 4.1 3.1 - - - +
216D SER* 3.7 23.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 143 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D SER 3.0 18.4 + - - +
140D ASP* 3.6 12.8 - - - +
142D LEU* 1.3 75.7 - - - +
144D ASN* 1.3 61.1 + - - +
146D ASN* 3.2 12.3 + - + +
147D ARG* 2.9 65.6 + - + +
214D TYR 5.0 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 144 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D ALA 5.3 0.7 - - - +
44D ALA* 3.0 35.1 + - - +
45D CYS 5.6 0.4 - - - -
50D LYS* 6.2 2.9 - - + +
140D ASP* 2.9 26.8 + - - +
141D VAL 3.8 2.0 - - - +
143D LEU* 1.3 78.4 - - - +
145D LEU* 1.3 65.7 + - - +
147D ARG* 3.2 35.1 + - + +
148D LEU* 2.9 28.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 145 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D VAL* 5.1 0.9 - - + -
14D LEU* 4.3 14.8 - - + -
40D ALA* 3.6 41.3 - - + +
41D VAL* 4.5 4.7 - - + +
44D ALA* 3.9 6.1 - - + -
141D VAL* 2.8 38.1 + - + +
142D LEU* 3.2 18.4 + - + +
144D ASN* 1.3 73.0 - - - +
146D ASN* 1.3 58.1 + - - +
148D LEU* 3.3 9.8 + - + +
149D ARG 3.0 21.5 + - - -
169D HIS* 3.6 11.2 - - - +
171D THR* 5.6 1.3 - - + -
172D VAL* 3.8 25.4 - - + -
214D TYR* 3.6 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 146 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142D LEU 2.9 13.3 + - - +
143D LEU* 3.5 14.0 - - + +
145D LEU* 1.3 75.8 - - - +
147D ARG* 1.3 60.8 + - + +
149D ARG* 2.9 37.7 + - - +
150D SER* 2.9 33.2 + - - -
214D TYR* 3.3 24.2 - - + +
215D THR* 3.5 22.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 147 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D LYS* 5.1 12.6 - - - +
143D LEU* 2.9 45.6 + - + +
144D ASN* 3.2 32.5 + - - +
146D ASN* 1.3 73.4 - - - +
148D LEU* 1.3 66.8 + - - +
149D ARG 3.3 0.2 + - - -
150D SER* 3.3 2.8 + - - -
151D ARG* 3.1 58.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
40D ALA* 3.6 29.6 - - - +
43D ALA* 4.0 13.7 - - + +
44D ALA 4.2 4.9 - - - +
50D LYS* 3.8 35.4 - - + +
144D ASN* 2.9 22.0 + - + +
145D LEU* 3.4 17.7 - - + +
146D ASN 3.2 0.2 - - - -
147D ARG* 1.3 77.1 - - - +
149D ARG* 1.3 63.8 + - - +
151D ARG 3.3 1.2 + - - -
152D ASP 3.0 3.3 + - - -
153D ILE* 2.9 65.6 + - + +
154D LEU* 4.7 1.6 - - + -
169D HIS* 3.9 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 149 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145D LEU 3.0 14.4 + - - +
146D ASN* 2.9 36.5 + - - +
148D LEU* 1.3 77.2 - - - +
150D SER* 1.3 62.3 + - - +
152D ASP* 3.0 14.4 + - - +
155D THR* 4.4 5.6 - - + +
167D ARG* 3.8 25.3 + - + +
169D HIS* 3.8 14.3 - - + -
210D LEU* 3.5 25.9 - - - +
211D ASP* 3.0 36.2 + - - +
214D TYR* 3.6 34.8 - - + +
215D THR* 5.3 0.6 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
146D ASN* 2.9 22.1 + - - -
147D ARG* 3.4 11.5 - - - -
149D ARG* 1.3 75.0 - - - +
151D ARG* 1.3 73.4 + - - +
152D ASP 3.3 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 151 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D LYS* 5.3 9.8 - - - +
147D ARG* 3.1 57.9 + - - +
149D ARG 3.2 0.8 - - - -
150D SER* 1.3 87.8 - - - +
152D ASP* 1.3 69.8 + - - +
153D ILE* 3.2 32.1 + - + +
----------------------------------------------------------
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