Contacts of the helix formed by residues 138 - 148 (chain B) in PDB entry 1OFY
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 THR 138 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B SER 3.8 6.5 - - - +
137B MET* 1.3 80.0 - - - +
139B PRO* 1.3 56.3 - - - +
140B GLU* 2.8 22.7 + - - +
141B GLN* 2.7 46.8 + - + +
142B MET* 2.7 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B MET 4.4 2.5 - - - +
138B THR* 1.3 84.5 - - - +
140B GLU* 1.3 67.4 + - + +
142B MET* 2.8 12.7 + - + +
143B GLN* 2.7 42.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B THR* 2.8 25.9 - - - +
139B PRO* 1.3 85.7 - - + +
141B GLN* 1.3 67.8 + - + +
143B GLN* 3.1 11.6 + - - +
144B LYS* 3.0 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B PHE* 4.1 4.4 - - - -
136B SER 3.5 3.6 - - - +
137B MET* 3.5 19.4 - - + -
138B THR* 2.7 58.0 + - + +
140B GLU* 1.3 73.1 - - + +
142B MET* 1.3 64.7 + - - +
144B LYS* 3.1 6.1 + - + +
145B GLY* 2.9 21.1 + - - -
150B LEU* 4.3 23.0 - - + +
154B ASP* 5.1 9.1 + - - +
158B LEU* 3.9 26.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B PHE* 3.7 15.0 - - - -
18B PRO* 3.9 28.9 - - + -
27B GLY* 4.6 16.8 - - - +
29B ALA* 4.0 10.8 - - + +
30B MET 3.9 18.4 - - - +
32B PRO* 3.7 26.7 - - + -
137B MET* 3.8 15.2 - - + -
138B THR 2.7 16.0 + - - +
139B PRO* 3.0 15.7 - - + +
141B GLN* 1.3 74.3 - - - +
143B GLN* 1.3 62.3 + - - +
145B GLY* 3.2 1.0 + - - -
146B ILE* 3.0 39.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ASN 3.0 29.4 + - - +
25B PRO* 3.4 26.2 + - - +
26B LYS 4.4 0.2 - - - -
27B GLY* 3.6 13.1 - - - +
139B PRO* 2.7 23.8 + - + +
140B GLU* 3.1 11.0 + - - +
142B MET* 1.3 75.6 - - - +
144B LYS* 1.3 56.5 + - + +
146B ILE* 3.2 11.1 + - - +
147B ASN* 2.7 50.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B GLU* 3.0 18.9 + - - +
141B GLN* 3.7 7.4 - - - +
143B GLN* 1.3 73.8 - - + +
145B GLY* 1.3 57.8 + - - +
147B ASN* 4.4 1.3 - - - +
148B GLY* 2.6 30.7 + - - -
149B THR* 2.9 44.4 + - - +
150B LEU* 3.3 30.0 + - + +
151B LEU* 5.2 0.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B PHE* 3.3 47.4 - - - +
19B VAL* 3.9 7.4 - - - +
141B GLN 2.9 12.5 + - - -
144B LYS* 1.3 76.7 - - - +
146B ILE* 1.3 63.6 + - - +
148B GLY* 3.3 11.3 + - - -
150B LEU* 3.8 7.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B PHE* 4.0 4.0 - - + -
18B PRO* 3.7 39.0 - - + +
19B VAL* 4.1 18.6 - - - +
20B GLY 4.6 7.8 + - - +
22B LYS 5.7 3.6 - - - +
24B ASN* 4.5 31.9 - - + +
27B GLY* 4.6 1.6 - - - -
142B MET* 3.0 49.1 + - + +
143B GLN* 3.6 18.8 - - - +
145B GLY* 1.3 80.8 - - - +
147B ASN* 1.3 68.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B PRO* 5.7 4.5 - - - +
24B ASN 5.9 0.7 + - - -
143B GLN* 2.7 45.6 + - - +
144B LYS* 4.3 1.8 - - - +
146B ILE* 1.3 82.8 - - - +
148B GLY* 1.3 61.2 + - - +
149B THR* 4.1 18.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B VAL* 6.0 2.2 - - - -
144B LYS 2.6 15.2 + - - -
145B GLY* 3.3 7.8 + - - -
146B ILE 3.2 3.6 - - - -
147B ASN* 1.3 76.6 - - - +
149B THR* 1.3 58.8 + - - +
150B LEU 3.5 3.7 - - - +
----------------------------------------------------------
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