Contacts of the helix formed by residues 129 - 140 (chain B) in PDB entry 2R5S
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 GLU 129 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU* 2.9 28.4 + - + +
127B GLN* 3.9 26.9 + - + +
128B GLY* 1.3 72.7 - - - +
130B HIS* 1.3 64.0 + - - +
131B ALA 3.4 2.6 + - - -
132B GLN* 2.9 33.9 + - - +
133B ALA* 3.1 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B LEU* 4.3 13.8 - - + +
128B GLY* 3.0 40.6 + - - -
129B GLU* 1.3 73.0 - - - +
131B ALA* 1.3 59.1 + - - +
133B ALA* 3.6 8.2 - - - +
134B LEU* 3.1 34.5 + - - +
156B ASP* 4.4 9.1 + - - -
157B CYS* 3.8 31.2 - - - +
160B GLU* 3.5 48.2 + - + +
161B THR* 5.1 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B GLU 3.4 0.6 - - - -
130B HIS* 1.3 76.6 - - - +
132B GLN* 1.3 65.4 + - - +
134B LEU* 3.4 10.9 + - + +
135B ASN* 3.4 20.8 + - - +
161B THR* 5.2 8.4 + - - +
265B LEU 6.1 1.6 - - - +
266B GLY* 6.4 2.2 - - - -
268B GLY* 5.8 10.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU* 3.6 30.4 - - + +
129B GLU* 2.9 43.0 + - - +
131B ALA* 1.3 79.0 - - - +
133B ALA* 1.3 61.9 + - - +
135B ASN* 3.3 6.4 + - - +
136B VAL* 3.1 26.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B VAL* 4.2 8.8 - - + +
124B LEU* 3.8 21.0 - - + +
125B LEU* 4.4 13.0 - - + +
129B GLU 3.1 17.8 + - - +
130B HIS* 3.6 6.5 - - - +
131B ALA 3.3 0.2 - - - -
132B GLN* 1.3 77.2 - - - +
134B LEU* 1.3 57.0 + - - +
136B VAL* 3.5 3.6 + - - +
137B ILE* 2.8 34.2 + - - +
157B CYS* 3.7 18.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B HIS 3.1 26.7 + - - +
131B ALA* 3.4 10.3 + - + +
133B ALA* 1.3 72.6 - - - +
135B ASN* 1.3 56.8 + - - +
137B ILE* 3.2 8.8 + - - +
138B GLN* 2.8 37.8 + - + +
154B LYS* 3.7 28.0 - - + -
157B CYS* 3.5 26.9 - - + +
158B LEU* 3.6 24.5 - - + -
161B THR* 4.6 3.6 - - + +
163B GLN* 4.4 20.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ALA 3.4 10.3 + - - +
132B GLN* 3.3 12.4 + - - +
134B LEU* 1.3 76.1 - - - +
136B VAL* 1.3 70.2 + - - +
138B GLN* 2.9 34.2 + - - +
139B THR* 3.1 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LEU* 3.5 42.2 - - + +
120B GLN* 4.2 10.3 - - + -
121B VAL* 3.5 11.2 - - + -
124B LEU* 3.6 19.3 - - + -
132B GLN* 3.1 16.3 + - + +
133B ALA 3.9 5.6 - - - +
135B ASN* 1.3 76.0 - - - +
137B ILE* 1.3 67.3 + - - +
139B THR* 2.9 28.6 + - - +
140B LEU* 3.4 7.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B MES 5.3 0.9 - - - +
118B LEU* 5.6 0.7 - - + -
121B VAL* 3.2 35.0 - - + -
133B ALA* 2.8 30.2 + - + +
134B LEU* 3.4 11.7 - - - +
135B ASN 3.2 0.2 - - - -
136B VAL* 1.3 75.5 - - - +
138B GLN* 1.3 63.2 + - + +
139B THR 3.2 1.2 + - - -
140B LEU* 3.4 14.3 + - + +
145B GLN* 3.3 25.0 - - + +
150B VAL* 3.9 32.3 - - + +
153B ALA* 4.8 9.9 - - + -
154B LYS* 4.3 33.7 - - + -
157B CYS* 5.5 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B LEU* 2.8 26.8 + - + +
135B ASN* 2.9 32.9 + - - +
137B ILE* 1.3 77.8 - - + +
139B THR* 1.3 63.3 + - - +
140B LEU 3.4 0.4 - - - +
145B GLN* 3.5 23.2 + - - +
154B LYS* 6.2 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ASP* 4.7 1.7 - - - +
117B LEU* 3.4 24.6 - - - +
135B ASN* 3.1 28.7 - - - +
136B VAL* 2.9 19.1 + - - +
138B GLN* 1.3 81.4 - - - +
140B LEU* 1.3 65.8 + - - +
141B SER 3.9 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ASP* 3.5 7.2 - - - +
117B LEU* 4.1 27.8 - - + -
118B LEU* 4.2 22.4 - - + +
121B VAL* 4.9 0.9 - - + -
136B VAL* 3.4 16.8 - - + +
137B ILE* 3.4 28.7 + - + +
138B GLN 4.2 0.3 - - - +
139B THR* 1.3 81.7 - - - +
141B SER* 1.3 70.7 + - - +
142B ASP 3.6 0.2 + - - -
144B LEU* 3.8 23.8 - - + -
145B GLN* 2.8 21.4 + - + +
150B VAL* 4.1 23.3 - - + -
----------------------------------------------------------
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