Contacts of the helix formed by residues 136 - 153 (chain A) in PDB entry 2FA5
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 136 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A PHE* 1.3 76.8 - - - +
137A ALA* 1.3 65.4 + - - +
138A GLU* 2.5 41.7 + - - -
139A GLU* 3.0 14.7 + - - +
140A GLN* 3.0 20.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A SER* 1.3 73.2 - - - +
138A GLU* 1.3 62.3 + - - +
140A GLN* 3.4 8.1 + - - +
141A GLN* 3.1 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A SER* 2.5 27.8 + - - +
137A ALA* 1.3 77.8 - - + +
139A GLU* 1.3 81.7 + - - +
141A GLN* 3.3 19.7 + - - +
142A THR* 3.0 32.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A VAL 3.9 0.2 - - - +
135A PHE* 3.3 16.7 - - + -
136A SER* 3.0 33.8 + - - +
138A GLU* 1.3 88.6 + - - +
140A GLN* 1.3 65.1 + - - +
142A THR* 3.2 8.5 + - - -
143A LEU* 3.0 23.7 + - - +
146B LEU* 4.1 11.3 - - + +
149B ARG* 2.6 44.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A GLU* 5.9 0.4 + - - -
132A MSE 3.4 44.6 - - + +
135A PHE* 4.0 13.4 - - + +
136A SER 3.0 12.3 + - - +
137A ALA* 3.7 11.1 - - - +
139A GLU* 1.3 77.5 - - - +
141A GLN* 1.3 61.1 + - - +
143A LEU* 3.3 4.5 + - - +
144A GLU* 2.9 51.6 + - - +
22B LEU* 5.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ALA 3.1 13.5 + - - +
138A GLU* 3.4 22.1 + - - +
140A GLN* 1.3 77.3 - - - +
142A THR* 1.3 56.9 + - - +
144A GLU* 3.2 15.1 + - - +
145A ARG* 2.9 47.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A GLU* 3.0 17.2 + - - -
139A GLU* 3.2 11.7 + - - -
141A GLN* 1.3 77.3 - - - +
143A LEU* 1.3 62.9 + - - +
145A ARG* 3.1 35.2 + - - +
146A LEU* 3.0 29.6 + - + +
142B THR* 4.0 17.5 - - + -
146B LEU* 4.0 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A MSE 4.2 13.2 - - + -
135A PHE* 3.7 27.4 - - + -
139A GLU 3.0 14.6 + - - +
140A GLN* 3.6 7.9 - - - +
142A THR* 1.3 75.8 - - - +
144A GLU* 1.3 59.0 + - - +
146A LEU* 3.3 2.8 + - - +
147A ILE* 3.0 47.2 + - + +
22B LEU* 4.3 14.1 - - + -
26B LEU* 5.8 1.8 - - + -
143B LEU* 4.0 24.2 - - + -
146B LEU* 3.8 23.3 - - + +
147B ILE* 5.2 5.6 - - + -
150B LEU* 3.8 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A GLN* 2.9 42.5 + - + +
141A GLN* 3.6 13.5 - - - +
143A LEU* 1.3 75.3 - - - +
145A ARG* 1.3 57.6 + - - +
147A ILE* 4.5 2.7 - - - -
148A ASP* 2.9 39.3 + - - +
20B GLN* 4.7 9.2 - - - +
22B LEU* 4.1 25.1 - - + +
25B ARG* 3.4 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A GLN* 2.9 42.1 + - + +
142A THR* 3.1 48.1 + - - +
144A GLU* 1.3 74.9 - - - +
146A LEU* 1.3 67.3 + - + +
148A ASP* 3.5 9.6 + - - +
149A ARG* 3.1 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A THR* 3.0 26.8 + - + +
143A LEU* 3.8 3.6 - - - +
145A ARG* 1.3 81.4 - - + +
147A ILE* 1.3 67.8 + - - +
149A ARG* 3.2 1.0 + - + -
150A LEU* 2.9 20.8 + - - +
135B PHE* 3.1 40.2 - - + -
139B GLU* 3.9 25.6 - - + +
142B THR* 3.9 16.4 - - + -
143B LEU* 3.8 44.9 - - + +
146B LEU* 4.6 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 4.8 5.4 - - + -
143A LEU* 3.0 34.7 + - + +
144A GLU* 3.9 4.5 - - - +
146A LEU* 1.3 76.7 - - - +
148A ASP* 1.3 64.1 + - - +
150A LEU* 3.2 9.7 + - + +
151A ALA* 3.0 22.9 + - + +
22B LEU* 5.5 3.8 - - + -
25B ARG* 4.1 31.6 - - + +
26B LEU* 3.8 30.5 - - + -
29B LEU* 3.9 23.1 - - + +
143B LEU* 4.2 21.5 - - + -
147B ILE* 6.0 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A GLU* 2.9 27.5 + - - +
145A ARG* 3.5 9.4 - - - +
147A ILE* 1.3 77.4 - - - +
149A ARG* 1.3 56.4 + - - +
151A ALA* 3.2 6.4 + - - +
152A LYS* 2.8 39.2 + - + +
25B ARG* 2.6 30.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ARG* 3.1 14.8 + - - +
146A LEU* 3.2 9.2 + - + +
148A ASP* 1.3 77.9 - - - +
150A LEU* 1.3 58.8 + - - +
152A LYS* 4.7 4.9 - - - +
153A ASP* 2.8 66.8 + - - -
154A GLY 3.3 4.2 + - - -
134B VAL* 4.3 16.5 - - + +
135B PHE* 3.6 26.7 - - + -
139B GLU* 5.7 3.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 4.3 22.0 - - + -
26A LEU* 4.9 2.5 - - + -
146A LEU 2.9 12.5 + - - +
147A ILE* 3.5 12.3 - - + +
149A ARG* 1.3 76.2 - - - +
151A ALA* 1.3 59.4 + - - +
154A GLY* 3.0 21.8 + - - +
155A LEU* 3.0 13.9 + - - +
29B LEU* 3.8 26.5 - - + -
33B ILE* 4.5 5.8 - - + -
131B LEU* 3.4 42.1 - - + +
132B MSE 4.0 5.4 - - - -
134B VAL* 4.8 0.7 - - + -
135B PHE* 3.4 20.8 - - + -
143B LEU* 4.3 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ILE* 3.0 18.1 + - + +
148A ASP* 3.2 6.0 + - - +
150A LEU* 1.3 78.2 - - - +
152A LYS* 1.3 79.0 + - - +
155A LEU* 3.5 33.0 - - + +
156A PRO* 4.1 1.0 - - - +
29B LEU* 4.1 15.2 - - + +
32B ARG* 6.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ASP* 2.8 27.7 + - + +
149A ARG* 4.3 4.3 - - - +
151A ALA* 1.3 90.4 + - - +
153A ASP* 1.3 68.0 + - - +
156A PRO* 3.4 17.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ARG* 2.8 47.1 + - - +
152A LYS* 1.3 82.4 - - - +
154A GLY* 1.3 65.9 + - - +
155A LEU 3.5 0.7 - - - -
156A PRO* 3.3 10.7 - - - +
157A ARG* 3.1 23.6 - - - +
134B VAL* 3.8 20.4 - - + -
----------------------------------------------------------
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