Contacts of the helix formed by residues 288 - 296 (chain B) in PDB entry 5H1C
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 288 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B ARG* 3.8 15.5 - - - -
242B GLN* 2.9 26.6 - - - +
245B LEU* 4.4 3.4 - - - +
287B ILE* 1.3 73.2 - - - +
289B GLY* 1.3 64.1 + - - +
291B ILE 3.8 3.8 + - - -
292B ILE* 3.5 22.5 + - - +
5D T 2.3 21.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B LYS* 6.1 4.3 - - - -
286B PRO* 4.4 5.3 + - - +
287B ILE 3.3 3.9 - - - +
288B GLY* 1.3 82.9 - - - +
290B ASN* 1.3 66.5 + - - +
291B ILE 3.4 0.2 + - - -
292B ILE* 3.7 6.2 + - - +
293B ALA* 3.7 9.9 + - - +
4D T 3.5 23.3 - - - -
5D T 3.0 12.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 290 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A GLU* 3.3 39.0 + - - +
229A ARG* 4.7 0.9 - - - +
269A VAL* 3.8 14.8 - - - +
271A ALA* 3.3 22.7 + - - +
284A LYS* 6.2 0.4 - - - +
289B GLY* 1.3 72.8 - - - -
291B ILE* 1.3 55.6 + - - +
293B ALA* 2.8 26.8 + - - +
294B HIS* 2.9 36.0 + - + +
4D T 3.1 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 291 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A ARG* 3.2 30.7 - - - +
230A THR* 6.1 0.9 - - + -
242B GLN* 3.3 51.4 - - + +
245B LEU* 4.8 3.1 - - + -
246B ALA* 4.0 31.6 - - + +
249B LEU* 3.8 8.4 - - + +
288B GLY 3.8 0.2 + - - -
289B GLY 3.3 1.4 - - - -
290B ASN* 1.3 77.1 - - - +
292B ILE* 1.3 64.4 + - + +
294B HIS* 3.9 3.1 + - - +
295B ALA* 3.6 18.2 + - - +
3D T 4.0 22.7 - - - +
4D T 3.8 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 292 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B GLU* 2.7 31.9 - - - +
225B THR* 3.7 25.8 - - + -
245B LEU* 4.6 11.9 - - + -
249B LEU* 3.8 23.6 - - + -
265B ILE* 5.8 5.4 - - + -
267B ASN* 3.9 4.7 - - - +
286B PRO* 6.0 2.0 - - + -
287B ILE 3.2 26.7 - - - +
288B GLY* 3.5 16.5 + - - +
289B GLY 3.7 5.7 + - - +
290B ASN 3.2 0.6 - - - -
291B ILE* 1.3 78.6 - - + +
293B ALA* 1.3 64.6 + - - +
295B ALA* 3.0 13.3 + - - +
296B SER* 3.4 10.8 + - - -
299B ARG* 3.9 4.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 293 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A GLU* 4.7 1.3 - - + +
129A PHE* 3.8 34.4 - - + +
602A ANP 4.0 0.2 + - - -
286B PRO* 6.2 2.0 - - + -
289B GLY 3.7 9.8 + - - +
290B ASN* 2.8 14.6 + - - +
292B ILE* 1.3 81.9 - - - +
294B HIS* 1.3 60.9 + - - +
295B ALA 3.3 0.5 + - - -
296B SER* 3.6 7.6 + - - -
299B ARG* 3.1 15.7 - - - +
316B ASP* 3.3 21.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 294 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A GLY 4.2 2.2 - - - -
128A GLU* 2.4 38.4 + - - -
129A PHE* 4.3 2.8 - - - +
133A LYS* 4.7 3.9 + - - -
163A GLU* 3.7 15.4 - - - +
229A ARG* 4.1 7.9 - - - +
268A GLN* 2.8 50.5 + - + +
269A VAL 3.6 16.7 + - - -
602A ANP 2.6 26.4 + - - -
290B ASN* 2.9 46.4 + - + +
291B ILE* 4.2 3.4 - - - +
292B ILE 3.3 0.2 - - - -
293B ALA* 1.3 76.3 - - - +
295B ALA* 1.3 63.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A GLU* 5.1 7.9 - - - +
165A THR* 5.9 2.1 - - - +
122B ILE* 5.0 13.4 - - + +
249B LEU* 4.1 24.0 - - + -
253B LEU* 5.1 15.6 - - + +
291B ILE 3.6 12.6 + - - +
292B ILE 3.0 10.1 + - - +
294B HIS* 1.3 81.4 - - - +
296B SER* 1.3 66.0 + - - +
297B THR* 3.4 5.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A THR* 6.1 0.2 - - - -
602A ANP 3.3 20.3 + - - -
122B ILE* 4.2 23.1 - - - -
124B GLU* 3.0 27.3 + - - -
265B ILE* 5.8 0.2 - - - -
292B ILE* 3.4 4.2 + - - -
293B ALA 3.6 2.9 + - - -
294B HIS 3.6 0.2 - - - -
295B ALA* 1.3 78.4 - - - +
297B THR* 1.3 63.6 + - - +
298B THR 2.9 21.0 + - - -
299B ARG* 3.1 14.8 + - - -
316B ASP* 3.9 5.0 + - - +
----------------------------------------------------------
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