Contacts of the helix formed by residues 297 - 309 (chain B) in PDB entry 1DBQ
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 297 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B TYR* 5.2 2.7 - - - +
77B ILE* 4.1 20.6 - - + -
145B MET* 3.6 11.0 - - + +
147B TRP* 4.1 27.6 - - + +
158B VAL* 4.3 10.8 - - + -
160B ASP* 5.7 2.9 - - + -
293B PRO 3.8 16.6 - - - +
294B LYS* 3.1 11.4 - - + +
296B SER* 1.3 79.3 - - - +
298B GLY* 1.3 54.6 + - - +
299B GLU 3.3 0.4 - - - -
300B THR* 3.7 2.7 - - - +
301B ALA* 2.7 36.1 + - - +
319B ILE* 4.2 27.9 - - + +
321B VAL* 4.2 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ILE* 4.2 17.4 - - - +
80B ALA* 4.3 4.0 - - - +
81B VAL* 4.0 24.6 - - - +
84B ASN* 4.4 2.0 - - - -
294B LYS 3.9 5.1 + - - -
296B SER 3.5 1.0 - - - +
297B LEU* 1.3 78.7 - - - +
299B GLU* 1.3 53.0 + - - +
301B ALA* 3.8 5.2 - - - +
302B PHE* 2.6 38.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ALA* 4.3 7.4 - - + +
83B LYS* 5.2 7.9 + - - +
84B ASN* 3.2 30.2 - - - +
295B ASP 5.0 6.0 - - - +
296B SER* 3.6 18.4 + - - +
297B LEU 3.3 0.2 - - - -
298B GLY* 1.3 74.8 - - - +
300B THR* 1.3 61.1 + - - +
303B ASN* 2.5 43.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B SER* 2.9 22.8 + - - -
297B LEU* 3.7 3.8 - - - -
299B GLU* 1.3 77.4 - - - +
301B ALA* 1.3 54.8 + - - +
303B ASN* 2.7 25.5 + - - +
304B MET* 2.7 28.1 + - + +
319B ILE* 3.1 33.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B VAL* 5.6 0.2 - - + -
120B LEU* 4.3 10.2 - - + +
143B VAL* 3.8 13.5 - - + +
145B MET* 3.6 35.0 - - + -
297B LEU 2.7 23.6 + - - +
298B GLY* 3.8 5.8 - - - +
300B THR* 1.3 75.3 - - - +
302B PHE* 1.3 56.2 + - - +
304B MET* 3.3 11.3 + - - +
305B LEU* 3.0 26.3 + - - +
319B ILE* 5.5 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ILE* 4.9 12.8 - - + -
81B VAL* 4.1 21.3 - - + -
84B ASN* 3.9 33.9 - - + +
85B CYS* 3.6 29.8 - - - -
88B LYS* 4.4 18.2 - - + -
90B TYR* 5.0 4.9 - + - -
120B LEU* 4.6 6.9 - - + +
298B GLY 2.6 23.8 + - - +
299B GLU 3.7 3.6 - - - +
301B ALA* 1.3 74.3 - - - +
303B ASN* 1.3 75.4 + - - +
305B LEU* 3.6 11.7 + - + +
306B LEU* 3.0 49.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ASN* 4.7 0.8 - - - +
299B GLU* 2.5 33.2 + - - +
300B THR* 2.7 10.1 + - + +
302B PHE* 1.3 98.2 - - - +
304B MET* 1.3 65.0 + - - +
305B LEU 3.0 1.3 - - - -
306B LEU* 3.0 17.5 + - + +
307B ASP* 3.1 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B VAL* 3.9 10.5 - - + -
156B ASP* 3.3 21.3 - - - +
300B THR* 2.7 23.3 + - + +
301B ALA* 3.6 10.1 - - - +
303B ASN* 1.3 76.5 - - - +
305B LEU* 1.3 63.7 + - - +
307B ASP* 4.1 4.5 - - - +
308B ARG* 2.9 34.9 + - - +
313B ARG* 3.7 21.4 + - - +
317B GLN* 3.2 36.1 - - + +
318B SER 5.1 0.4 - - - -
319B ILE* 3.0 35.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ILE* 3.7 37.9 - - + -
118B GLY* 3.8 5.6 - - - -
119B LEU 2.8 41.5 - - - +
120B LEU* 4.2 9.0 - - + -
141B PRO 4.3 1.6 - - - +
142B MET* 3.4 32.5 - - - +
143B VAL* 3.4 5.3 - - + +
301B ALA 3.0 13.7 + - - +
302B PHE* 3.6 16.2 - - + +
303B ASN 3.0 0.2 - - - -
304B MET* 1.3 78.5 - - - +
306B LEU* 1.3 70.6 + - + +
308B ARG* 3.3 3.5 - - + +
309B ILE* 3.0 21.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LYS* 5.1 0.2 - - - +
62B ILE* 4.7 15.0 - - + -
88B LYS* 5.5 4.3 - - + -
90B TYR* 4.4 18.6 - - + +
302B PHE* 3.0 50.7 + - + +
303B ASN* 3.0 14.1 + - + +
305B LEU* 1.3 81.7 - - + +
307B ASP* 1.3 54.8 + - - +
309B ILE* 2.6 54.0 + - + +
310B VAL* 2.9 13.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B ASN 3.1 12.1 + - - +
304B MET* 4.1 4.5 - - - +
306B LEU* 1.3 76.7 - - - +
308B ARG* 1.3 64.6 + - - +
310B VAL* 3.5 9.8 - - - +
311B ASN* 2.8 63.8 + - - +
312B LYS 3.3 3.3 + - - -
313B ARG* 3.0 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 308 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B PRO* 4.8 7.3 - - + +
142B MET 2.8 38.8 + - - +
143B VAL* 3.9 3.2 - - - +
154B PHE* 5.1 3.4 + - - -
156B ASP* 2.8 41.1 + - - -
304B MET* 2.9 26.2 + - - +
305B LEU* 3.3 7.6 - - + +
306B LEU 2.9 0.4 - - - -
307B ASP* 1.3 79.4 - - - +
309B ILE* 1.3 62.4 + - - +
312B LYS* 3.3 17.5 - - - -
313B ARG* 3.0 53.1 + - + +
314B GLU* 4.8 5.8 + - - +
315B GLU 3.5 1.0 + - - -
316B PRO* 3.0 28.9 - - - +
317B GLN 3.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 309 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LYS* 4.2 18.2 - - - +
117B ASP* 3.1 24.5 - - + +
118B GLY* 4.0 4.5 - - - -
141B PRO* 3.0 41.1 - - + -
305B LEU* 3.0 16.0 + - + +
306B LEU* 2.6 52.0 + - + +
308B ARG* 1.3 74.6 - - - +
310B VAL* 1.3 81.1 + - + +
312B LYS* 4.1 6.2 + - - +
----------------------------------------------------------
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