Contacts of the helix formed by residues 281 - 297 (chain B) in PDB entry 3HS3
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 ASN 281 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ARG* 5.6 1.3 - - - +
279B ASP* 2.9 17.2 + - - +
280B GLN* 1.3 79.7 - - - +
282B PRO* 1.3 67.5 - - - +
283B LYS* 3.9 7.3 + - - +
284B LEU* 3.0 51.3 + - + +
285B ILE* 3.1 9.7 + - - +
308B ILE* 4.7 1.6 - - + -
309B ASP 4.5 9.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ARG* 3.5 34.1 - - - +
73B PHE* 3.4 41.1 - - + +
76B GLN* 3.5 21.8 - - + +
77B ILE* 3.5 9.4 - - + +
279B ASP* 3.8 0.2 - - - +
280B GLN* 3.4 11.9 - - + +
281B ASN* 1.3 89.8 - - - +
283B LYS* 1.3 60.8 + - - +
285B ILE* 3.1 13.7 + - + +
286B GLY 2.9 18.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 283 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B GLN* 3.4 38.4 + - - +
79B ASP* 2.8 32.5 + - - -
80B GLY* 3.6 10.4 - - - +
83B GLU* 3.7 17.9 + - - +
281B ASN* 3.2 7.0 - - - +
282B PRO* 1.3 80.8 - - - +
284B LEU* 1.3 58.8 + - - +
286B GLY 3.2 1.4 + - - -
287B GLN* 2.9 54.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 284 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B ASN* 3.0 38.7 + - + +
283B LYS* 1.3 76.2 - - - +
285B ILE* 1.3 63.8 + - - +
287B GLN* 3.6 20.4 - - + +
288B THR* 2.7 45.9 + - - +
308B ILE* 3.8 24.2 - - + -
309B ASP* 5.6 2.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 285 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B PHE* 4.0 27.6 - - + -
77B ILE* 4.2 11.7 - - + -
140B TYR* 4.1 20.4 - - + -
141B ASP* 4.8 5.8 - - - +
152B ILE* 3.7 24.4 - - + +
154B SER* 4.2 21.8 - - - +
280B GLN* 3.6 19.5 - - + +
281B ASN 3.1 10.3 + - - +
282B PRO* 3.1 9.8 + - + +
284B LEU* 1.3 78.1 - - - +
286B GLY* 1.3 57.1 + - - +
289B ALA* 3.0 27.5 + - - +
308B ILE* 4.2 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ILE* 3.4 29.8 - - - -
81B ILE* 3.3 22.1 - - - +
282B PRO 2.9 11.4 + - - -
283B LYS 3.6 2.5 - - - -
285B ILE* 1.3 76.5 - - - +
287B GLN* 1.3 64.4 + - - +
289B ALA* 3.2 2.8 + - - +
290B ALA* 3.1 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B GLY* 3.6 23.9 - - - +
83B GLU* 2.8 26.2 + - - +
84B VAL* 3.9 11.8 - - + +
283B LYS* 2.9 36.7 + - - +
284B LEU* 3.4 28.4 + - + +
286B GLY* 1.3 71.6 - - - +
288B THR* 1.3 57.9 + - - +
290B ALA* 3.2 4.3 + - - +
291B HIS* 2.9 40.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B ILE* 3.9 6.1 - - + -
284B LEU* 2.7 35.7 + - - +
285B ILE 3.8 3.4 - - - -
287B GLN* 1.3 75.2 - - - +
289B ALA* 1.3 65.7 + - - +
291B HIS* 3.2 8.9 + - + +
292B ARG* 2.9 27.7 + - + +
306B SER* 3.7 33.7 - - - +
308B ILE* 3.7 16.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ILE* 4.7 2.0 - - + -
121B ILE* 4.1 22.3 - - + +
138B VAL* 3.9 13.1 - - + +
140B TYR* 4.7 7.4 - - + -
152B ILE* 3.6 23.1 - - + +
285B ILE 3.0 18.0 + - - +
286B GLY* 3.5 8.5 - - - +
288B THR* 1.3 76.3 - - - +
290B ALA* 1.3 57.9 + - - +
292B ARG* 3.5 1.6 + - - +
293B LEU* 3.0 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 290 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ILE* 4.0 10.5 - - + +
84B VAL* 3.6 26.0 - - + -
85B ILE* 3.8 18.1 - - + +
121B ILE* 4.1 10.0 - - - +
286B GLY 3.1 11.9 + - - +
287B GLN 3.5 8.3 - - - +
288B THR 3.2 0.2 - - - -
289B ALA* 1.3 75.6 - - - +
291B HIS* 1.3 60.6 + - - +
293B LEU* 3.2 3.3 + - - +
294B LEU* 2.9 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 291 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B VAL* 3.7 30.3 - - + +
287B GLN* 2.9 36.3 + - + +
288B THR* 3.7 8.3 - - + +
290B ALA* 1.3 75.1 - - - +
292B ARG* 1.3 65.4 + - + +
294B LEU* 3.3 10.2 + - - +
295B ASP* 3.1 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 292 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B VAL* 4.1 3.4 - - + -
150B VAL* 3.5 37.2 - - + +
152B ILE* 3.8 9.2 - - + -
288B THR* 2.9 23.3 + - + +
289B ALA 3.9 3.4 - - - +
291B HIS* 1.3 78.3 - - + +
293B LEU* 1.3 62.3 + - - +
295B ASP* 3.3 19.9 + - - +
296B LEU* 3.1 26.0 + - - +
300B ASN* 5.3 6.3 - - - +
302B SER* 3.9 16.2 + - - -
304B ARG* 2.8 35.3 + - - +
305B ASN 3.8 1.4 + - - -
306B SER* 2.7 46.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 293 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ILE* 3.7 36.3 - - + -
85B ILE* 5.9 2.2 - - + -
119B GLY* 4.0 5.8 - - - -
120B ILE 3.7 11.7 - - - +
121B ILE* 3.7 23.6 - - + -
136B PRO* 3.6 37.2 - - + +
137B LEU 4.1 0.4 - - - +
138B VAL* 3.7 15.6 - - + +
289B ALA 3.0 18.7 + - - +
290B ALA* 3.2 6.3 + - - +
292B ARG* 1.3 74.1 - - - +
294B LEU* 1.3 65.6 + - + +
296B LEU* 3.1 4.2 + - + +
297B MET* 2.9 34.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 294 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ILE* 5.8 1.8 - - + -
84B VAL* 4.1 23.1 - - + +
85B ILE* 5.2 8.7 - - + -
88B GLU* 4.3 18.4 - - + -
90B TYR* 3.9 30.3 - - + +
290B ALA 2.9 21.2 + - - +
291B HIS* 3.7 11.0 - - - +
293B LEU* 1.3 77.6 - - + +
295B ASP* 1.3 57.7 + - - +
297B MET* 3.3 21.2 + - + +
298B SER* 2.7 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B HIS* 3.1 22.5 + - - +
292B ARG* 3.4 26.1 + - - +
293B LEU 3.1 0.2 - - - -
294B LEU* 1.3 76.3 - - - +
296B LEU* 1.3 60.4 + - + +
298B SER* 2.9 21.3 + - - -
300B ASN* 3.1 45.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B PRO* 4.0 18.3 - - + +
137B LEU 3.4 34.5 - - - +
138B VAL* 3.8 15.3 - - + -
150B VAL* 3.8 28.0 - - + -
292B ARG* 3.1 11.6 + - - +
293B LEU* 3.5 7.0 - - - +
295B ASP* 1.3 75.8 - - + +
297B MET* 1.3 59.7 + - - +
298B SER 3.2 3.8 + - - -
299B GLY* 3.3 11.4 + - - -
300B ASN* 3.2 20.9 + - - +
301B ASN* 4.5 9.2 - - - +
302B SER 4.1 7.0 - - - +
303B THR* 6.0 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B LYS* 6.1 0.5 - - - -
62B ILE* 3.9 11.0 - - + -
90B TYR* 3.2 42.0 - - + +
118B ASP* 3.6 34.8 - - + +
136B PRO* 3.9 15.9 - - + -
293B LEU* 2.9 39.6 + - - +
294B LEU* 3.5 16.4 - - + +
295B ASP 3.2 0.4 - - - -
296B LEU* 1.3 76.6 - - - +
298B SER* 1.3 59.5 + - - +
299B GLY 3.5 1.1 + - - -
----------------------------------------------------------
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