Contacts of the helix formed by residues 300 - 314 (chain B) in PDB entry 3NUI
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 300 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B PHE* 3.7 20.9 - - - -
108B SER 3.9 2.5 - - - -
279B ASP 2.8 22.7 + - - -
299B LEU* 1.3 72.3 - - - +
301B PRO* 1.3 72.5 - - - +
302B GLU* 3.4 4.2 + - - -
303B LEU* 3.6 1.6 + - - +
304B SER* 2.6 31.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B PHE* 4.1 12.3 - - + -
107B ASP* 5.0 6.1 - - + +
108B SER* 3.4 38.3 - - - +
300B GLY* 1.3 81.7 - - - +
302B GLU* 1.3 75.9 + - - +
304B SER* 3.6 6.0 - - - -
305B LYS* 3.1 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B PHE* 5.6 1.0 - - - -
247B ARG* 5.0 1.4 + - - -
279B ASP* 3.0 37.3 - - + +
300B GLY* 4.1 2.3 - - - -
301B PRO* 1.3 95.0 - - - +
303B LEU* 1.3 61.8 + - + +
305B LYS* 3.3 4.2 + - - +
306B ARG* 3.1 38.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B MET* 5.0 1.1 - - - -
127B MET* 5.5 3.3 - - + +
128B LEU* 4.6 8.1 - - + -
131B LEU* 4.0 25.7 - - + +
252B PRO* 4.4 20.9 - - + -
254B ILE* 4.2 11.9 - - + -
279B ASP* 3.9 35.7 - - + +
280B ALA* 4.0 15.3 - - + -
299B LEU* 4.0 21.7 - - + +
300B GLY 3.6 3.9 + - - +
301B PRO 3.5 0.2 - - - -
302B GLU* 1.3 78.6 - - + +
304B SER* 1.3 61.7 + - - +
306B ARG* 4.1 14.3 - - - +
307B LEU* 2.9 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B GLY* 3.4 4.9 - - - -
110B ARG* 3.4 31.7 + - - +
299B LEU* 3.3 21.4 + - - +
300B GLY 2.6 23.5 + - - -
301B PRO* 3.6 7.4 - - - -
303B LEU* 1.3 77.0 - - - +
305B LYS* 1.3 67.3 + - - +
307B LEU* 3.3 2.2 + - - +
308B GLU* 3.0 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B PRO* 3.1 14.9 + - - +
302B GLU* 3.9 4.5 - - - +
304B SER* 1.3 82.3 - - - +
306B ARG* 1.3 53.7 + - + +
308B GLU* 3.2 36.9 + - + -
309B THR* 2.7 58.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B LEU* 3.3 26.3 - - + +
132B HIS* 3.8 23.4 + - - -
135B GLU* 2.7 36.6 + - - +
140B LYS* 5.7 1.0 - - - +
250B ASP* 4.3 20.2 + - - +
252B PRO* 4.6 10.5 - - - +
302B GLU* 3.1 28.1 + - - +
303B LEU* 4.1 14.8 - - - +
305B LYS* 1.3 74.6 - - + +
307B LEU* 1.3 57.1 + - - +
309B THR* 3.8 7.6 + - - -
310B ALA* 2.9 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ARG* 4.5 6.3 - - - +
112B PHE* 3.7 36.1 - - + -
127B MET* 3.9 27.4 - - + +
130B PHE* 4.0 29.2 - - + -
131B LEU* 3.9 10.7 - - + +
299B LEU* 3.9 4.3 - - + -
303B LEU 2.9 21.3 + - - +
304B SER* 3.6 4.9 - - - +
306B ARG* 1.3 76.7 - - - +
308B GLU* 1.3 51.7 - - + +
310B ALA* 3.2 2.1 + - - +
311B ILE* 2.8 51.8 + - + +
318B PRO* 4.6 4.3 - - + -
321B PHE* 4.8 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 308 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ARG* 2.9 49.0 - - - +
304B SER* 3.0 14.2 + - - +
305B LYS* 3.4 33.6 + - + +
307B LEU* 1.3 74.0 - - - +
309B THR* 1.3 63.1 + - + +
311B ILE* 3.3 7.5 + - - +
312B GLU* 3.2 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 309 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B GLU* 5.6 0.9 + - - -
305B LYS* 2.7 56.4 + - + +
306B ARG* 3.9 7.3 + - - -
308B GLU* 1.3 74.2 - - - +
310B ALA* 1.3 58.2 + - - +
312B GLU* 4.0 11.0 - - - +
313B ALA* 3.1 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B PHE* 4.6 6.7 - - + -
131B LEU* 3.9 15.3 - - + +
134B ALA* 3.7 26.6 - - + +
135B GLU* 4.9 6.3 - - + -
306B ARG 2.9 19.2 + - - +
307B LEU 3.8 2.5 - - - +
309B THR* 1.3 75.8 + - - +
311B ILE* 1.3 65.0 + - - +
312B GLU 3.2 1.6 - - - -
313B ALA* 4.3 5.6 - - - +
314B ILE* 3.1 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ARG* 4.7 8.7 - - - +
130B PHE* 4.2 4.3 - - + -
307B LEU* 2.8 44.7 + - + +
308B GLU* 3.7 7.2 - - - +
310B ALA* 1.3 71.8 - - - +
312B GLU* 1.3 62.1 + - + +
314B ILE* 4.2 0.2 - - - -
315B GLU* 3.2 19.2 + - - -
316B GLU 3.3 22.6 + - - +
317B PHE* 3.8 32.3 - - + -
318B PRO* 3.6 34.8 - - + -
321B PHE* 5.8 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B GLU* 3.2 23.4 + - - +
309B THR* 4.0 11.1 - - - +
310B ALA 3.2 0.4 - - - -
311B ILE* 1.3 82.4 - - + +
313B ALA* 1.3 62.9 + - - +
314B ILE 3.3 0.4 - - - -
315B GLU* 3.1 23.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B ALA 5.6 6.5 - - - +
309B THR 3.1 19.9 + - - +
310B ALA* 3.5 6.0 + - - +
312B GLU* 1.3 76.7 - - - +
314B ILE* 1.3 60.4 + - - +
315B GLU* 4.7 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A VAL* 4.6 16.4 - - + +
130B PHE* 4.1 20.4 - - + +
133B ALA* 6.3 0.7 - - + -
134B ALA* 3.8 31.8 + - + +
310B ALA 3.1 23.1 + - - +
311B ILE 3.6 0.7 - - - +
313B ALA* 1.3 75.4 - - - +
315B GLU* 1.3 67.5 + - - +
316B GLU* 3.0 43.8 + - + +
----------------------------------------------------------
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