Contacts of the helix formed by residues 140 - 154 (chain B) in PDB entry 5FS9
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 GLY 140 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B GLY 3.5 4.2 + - - -
139B GLY* 1.3 79.4 - - - +
141B THR* 1.3 61.6 + - - -
142B ALA 3.5 2.0 - - - -
143B ALA* 3.5 3.0 + - - +
144B PHE* 3.0 30.1 + - - +
169B PRO* 4.2 1.8 - - - +
170B TYR 5.0 4.7 - - - -
172B ARG* 5.0 3.4 - - - -
205B PHE* 4.6 5.8 - - - -
259B ALA 5.0 0.4 + - - -
1000B FAD 3.4 27.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B GLY* 1.3 69.7 - - - -
142B ALA* 1.3 67.2 + - - +
144B PHE* 3.4 2.8 + - - +
145B ALA* 3.0 23.2 + - - +
170B TYR 3.9 6.7 + - - -
171B MET* 4.5 2.1 - - - -
172B ARG 5.0 0.9 + - - -
205B PHE* 3.5 26.3 - - + -
455B HIS* 3.9 20.9 + - + +
458B ALA* 3.6 16.8 - - + -
459B VAL* 3.7 25.1 - - + -
1000B FAD 3.2 30.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B THR* 1.3 74.9 - - - +
143B ALA* 1.3 58.1 + - - +
145B ALA 3.3 0.3 + - - -
146B ALA* 3.0 30.0 + - - +
257B LEU* 4.7 0.9 - - - -
259B ALA* 4.1 9.9 - - + -
436B ALA* 4.1 10.8 - - + -
437B GLY* 3.9 26.9 - - - +
458B ALA* 3.4 22.4 - - + +
462B GLY* 3.4 5.0 - - - -
1000B FAD 2.8 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LEU* 3.3 22.8 - - + +
138B GLY 3.0 31.2 - - - +
139B GLY* 4.3 2.2 - - - -
140B GLY 3.5 10.6 + - - +
141B THR 3.3 0.6 - - - -
142B ALA* 1.3 77.8 - - - +
144B PHE* 1.3 58.1 + - - +
146B ALA 3.3 0.5 + - - -
147B ALA* 2.9 25.6 + - - +
161B ILE* 4.4 6.7 - - + -
257B LEU* 4.4 7.4 - - - -
259B ALA* 3.9 14.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B GLY 3.0 18.1 + - - +
141B THR 3.8 3.1 - - - +
143B ALA* 1.3 76.1 - - - +
145B ALA* 1.3 68.5 + - + +
147B ALA* 3.2 8.3 + - + +
148B ARG* 3.1 51.5 + - + +
161B ILE* 4.6 6.2 - - + +
169B PRO* 4.1 8.7 - - + +
205B PHE* 3.6 50.3 - + + -
206B GLN* 3.7 25.6 - - + -
210B PHE* 4.2 10.3 - + - -
211B TYR* 3.5 28.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B THR 3.0 17.0 + - - +
142B ALA 3.8 3.6 - - - +
144B PHE* 1.3 83.9 - - + +
146B ALA* 1.3 57.5 + - - +
148B ARG* 3.5 5.7 + - - +
149B SER* 3.0 28.4 + - - -
458B ALA 4.3 0.2 - - - +
459B VAL* 3.5 41.7 - - + +
462B GLY* 4.1 2.7 - - - -
463B ARG* 4.0 10.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LEU* 4.3 5.6 - - + -
142B ALA 3.0 16.6 + - - +
143B ALA 3.6 3.6 - - - +
145B ALA* 1.3 74.5 - - - +
147B ALA* 1.3 60.1 + - - +
149B SER* 3.2 2.9 + - - -
150B ILE* 2.8 38.2 + - + +
257B LEU* 3.4 25.1 - - + -
462B GLY 3.2 23.5 + - - +
466B GLY* 4.4 7.4 - - - +
469B MET* 5.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LEU* 3.7 17.1 - - + +
143B ALA 2.9 17.1 + - - +
144B PHE* 3.6 7.4 - - + +
146B ALA* 1.3 75.8 - - - +
148B ARG* 1.3 63.1 + - + +
150B ILE* 3.4 3.5 + - - +
151B ARG* 3.0 29.5 + - - +
159B VAL* 4.1 8.4 - - + +
161B ILE* 4.2 5.8 - - + -
210B PHE* 6.3 0.7 - - + -
225B VAL* 4.0 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B PHE* 3.1 39.7 + - + +
145B ALA* 3.8 8.1 - - - +
147B ALA* 1.3 77.0 - - + +
149B SER* 1.3 58.9 + - - +
151B ARG* 3.4 7.6 + - - +
152B ALA* 3.0 28.9 + - - +
206B GLN* 4.3 13.7 - - - +
210B PHE* 3.6 39.9 - - + -
225B VAL* 6.2 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ALA 3.0 18.1 + - - -
146B ALA 3.2 4.7 + - - -
148B ARG* 1.3 74.3 - - - +
150B ILE* 1.3 65.4 + - - +
152B ALA* 3.2 6.1 + - - +
153B ARG* 3.0 30.0 + - - +
463B ARG* 2.8 41.9 + - - +
466B GLY* 4.1 3.4 - - - -
467B GLU* 3.5 17.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B PHE* 3.9 38.4 - - + -
136B LEU* 4.1 21.3 - - + -
146B ALA 2.8 26.0 + - - +
147B ALA* 3.7 6.5 - - - +
149B SER* 1.3 75.6 - - - +
151B ARG* 1.3 58.0 + - - +
153B ARG* 3.3 1.6 + - - +
154B ASP* 2.8 30.3 + - - +
157B ALA* 3.7 22.2 - - + -
159B VAL* 3.9 11.2 - - + -
466B GLY* 3.7 20.4 - - - +
469B MET* 4.2 12.3 - - + -
470B THR* 4.1 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ALA 3.0 20.8 + - - +
148B ARG* 3.8 7.4 - - - +
150B ILE* 1.3 77.5 - - - +
152B ALA* 1.3 60.1 + - - +
154B ASP 3.9 3.4 - - - -
155B PRO* 3.1 44.8 + - - +
157B ALA* 2.9 38.2 + - - +
159B VAL* 4.5 4.3 - - + -
210B PHE* 6.3 0.9 - - + -
222B ASN* 3.0 26.5 + - - +
223B GLY 4.1 1.4 + - - -
224B GLY* 3.5 21.2 - - - +
225B VAL* 3.7 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B ARG 3.0 17.3 + - - +
149B SER* 3.2 7.8 + - - +
151B ARG* 1.3 77.8 - - - +
153B ARG* 1.3 62.6 + - + +
155B PRO* 4.4 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B SER* 3.0 19.4 + - - +
150B ILE 3.8 2.9 - - - +
152B ALA* 1.3 79.5 - - + +
154B ASP* 1.3 59.8 + - - +
155B PRO* 3.6 6.9 - - - +
467B GLU* 3.7 25.8 + - + +
470B THR* 3.0 48.1 + - - +
471B GLY 4.0 1.4 - - - -
472B ALA* 3.5 34.8 - - - +
474B LYS* 5.1 5.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B PHE* 4.0 21.7 - - - -
150B ILE 2.8 12.1 + - - +
151B ARG* 3.5 6.9 - - - +
153B ARG* 1.3 76.6 - - - +
155B PRO* 1.3 61.3 - - - +
156B GLY* 3.6 9.4 + - - -
157B ALA* 2.9 35.4 + - + +
470B THR* 4.3 14.9 - - + +
----------------------------------------------------------
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