Contacts of the helix formed by residues 135 - 146 (chain D) in PDB entry 5SWW
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 LEU 135 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B GLN* 3.2 31.6 - - + +
187B SER* 5.7 0.2 - - - -
188B GLY* 3.9 11.7 - - - +
102D PHE* 3.2 38.5 - - + +
103D SER* 3.7 14.6 - - - +
133D ASP* 3.0 7.9 + - - -
134D PRO* 1.3 85.6 - - + +
136D TYR* 1.3 63.1 + - - +
137D LYS 3.2 2.0 - - - -
138D GLU* 3.2 32.7 + - + +
139D ALA 3.0 17.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 136 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D SER* 5.0 5.4 - - - +
100D PRO 5.4 1.8 - - - +
101D CYS* 5.9 0.7 - - - +
129D ILE* 3.5 20.4 - - + -
130D TYR* 3.3 22.7 - - + +
131D ASP* 3.6 20.1 - - + +
133D ASP* 3.1 25.1 + - + +
134D PRO* 4.4 8.5 - - + -
135D LEU* 1.3 75.0 - - - +
137D LYS* 1.3 110.4 + - + +
139D ALA* 3.0 10.6 + - - +
140D LEU* 2.9 28.5 + - + +
189D ARG* 3.2 30.0 + - - -
193D ILE* 3.7 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 137 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D PRO 6.0 0.4 - - - +
135D LEU* 3.2 0.8 - - - +
136D TYR* 1.3 116.6 - - + +
138D GLU* 1.3 64.3 + - - +
140D LEU* 3.3 1.8 + - - -
141D GLN* 2.9 44.0 + - - +
193D ILE* 3.6 36.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 138 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B GLN* 5.1 7.4 - - - +
102D PHE* 3.7 24.9 - - + -
134D PRO 4.4 1.6 - - - +
135D LEU* 3.2 45.8 + - + +
137D LYS* 1.3 83.5 - - - +
139D ALA* 1.3 57.8 + - - +
141D GLN* 4.0 14.2 - - - +
142D MET* 2.9 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 139 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D PRO 3.2 26.5 - - - +
101D CYS 3.6 7.4 - - - +
102D PHE* 3.5 24.6 - - + +
107D ALA* 3.8 7.7 - - + +
135D LEU 3.0 7.3 + - - +
136D TYR* 3.0 11.6 + - - +
138D GLU* 1.3 74.5 - - - +
140D LEU* 1.3 61.6 + - + +
142D MET* 3.3 2.3 + - - +
143D LEU* 2.9 36.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 140 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D SER* 4.0 26.5 - - - +
100D PRO* 5.1 3.4 - - + +
126D ALA* 5.9 1.6 - - + -
129D ILE* 4.7 13.0 - - + -
136D TYR* 2.9 27.3 + - + +
137D LYS 3.9 3.1 - - - +
139D ALA* 1.3 74.0 - - - +
141D GLN* 1.3 58.4 + - - +
143D LEU* 3.3 13.5 + - + +
144D ARG* 2.9 28.6 + - - +
150D VAL* 3.7 25.7 - - + +
152D ILE* 6.4 1.8 - - + -
190D LEU* 3.6 27.8 - - + -
193D ILE* 3.7 28.9 - - + -
194D LEU* 3.8 4.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 141 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D LYS* 2.9 29.2 + - - +
138D GLU* 4.0 16.6 - - - +
140D LEU* 1.3 75.8 - - - +
142D MET* 1.3 56.0 + - - +
144D ARG* 3.3 16.1 + - - +
145D ASP* 2.9 38.5 + - - +
193D ILE* 3.3 37.9 + - + +
194D LEU* 4.0 7.9 - - + -
196D ASN* 4.1 13.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 142 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B GLU* 3.7 21.1 - - + +
102D PHE* 3.5 26.5 - - + -
107D ALA* 3.7 15.0 - - + +
108D GLY* 3.6 34.1 - - - -
111D ARG* 4.1 24.6 - - + +
138D GLU 2.9 19.6 + - - +
139D ALA 3.8 3.4 - - - +
141D GLN* 1.3 76.0 - - - +
143D LEU* 1.3 64.8 + - - +
145D ASP* 3.4 8.6 + - - +
146D ALA* 3.2 21.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
100D PRO* 3.6 38.6 - - + +
107D ALA* 4.1 18.2 - - + +
110D VAL* 3.7 38.1 - - + -
111D ARG* 5.1 1.3 - - - +
114D LEU* 5.9 0.4 - - + -
124D ILE* 3.7 18.4 - - + -
139D ALA 2.9 25.0 + - - +
140D LEU* 3.6 11.4 - - + +
142D MET* 1.3 75.1 - - - +
144D ARG* 1.3 63.0 + - - +
146D ALA* 3.4 8.7 + - - +
148D ALA* 3.3 28.3 + - + +
150D VAL* 3.8 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 144 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D LEU 2.9 16.2 + - - +
141D GLN* 3.6 17.5 + - - +
142D MET 3.3 0.2 - - - -
143D LEU* 1.3 77.7 - - - +
145D ASP* 1.3 81.6 + - - +
146D ALA 3.1 4.5 + - - -
147D GLY* 3.1 14.4 + - - -
148D ALA 3.5 12.3 + - - +
150D VAL* 3.8 7.1 - - + +
194D LEU* 3.3 49.1 + - + +
196D ASN* 3.0 62.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 145 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D ARG* 5.9 0.7 - - - -
141D GLN* 2.9 25.6 + - - +
142D MET* 3.4 8.4 + - - +
144D ARG* 1.3 103.1 + - - +
146D ALA* 1.3 57.2 + - - +
147D GLY 3.3 1.9 + - - -
196D ASN* 5.5 0.2 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
111D ARG* 3.6 31.2 - - + +
114D LEU* 3.6 32.4 - - + +
115D GLN* 5.9 2.8 - - + +
142D MET 3.2 15.4 + - - +
143D LEU* 3.7 7.6 - - - +
144D ARG 3.1 1.6 - - - -
145D ASP* 1.3 77.3 - - - +
147D GLY* 1.3 59.8 + - - +
148D ALA 3.4 0.4 - - - -
----------------------------------------------------------
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