Contacts of the helix formed by residues 187 - 200 (chain A) in PDB entry 2HKU
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 SER 187 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A LYS* 3.9 1.6 - - - -
182A GLU* 3.6 25.2 - - - +
183A SER* 3.9 1.7 - - - +
186A TYR* 1.3 78.8 - - - +
188A LEU* 1.3 66.4 + - - +
189A GLU* 3.7 6.9 + - - +
190A GLU* 2.7 37.6 + - - +
191A ALA* 2.9 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A GLY* 4.8 6.3 - - - +
102A LEU* 3.7 42.0 - - + +
103A GLY* 4.1 10.3 - - - +
177A LYS* 3.9 14.0 - - + +
182A GLU* 4.7 7.5 - - + +
187A SER* 1.3 74.9 - - - +
189A GLU* 1.3 62.9 + - - +
191A ALA* 3.3 0.9 + - - +
192A VAL* 3.0 31.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A SER* 3.3 7.4 + - - +
188A LEU* 1.3 80.1 - - - +
190A GLU* 1.3 64.7 + - + +
192A VAL* 3.5 5.4 + - - +
193A ALA* 3.0 19.6 + - - +
304A EDO 3.4 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A SER* 5.2 1.2 - - - -
185A GLY* 3.2 42.0 + - - +
187A SER* 2.7 36.9 + - - +
189A GLU* 1.3 79.8 - - + +
191A ALA* 1.3 57.9 + - - +
193A ALA* 3.2 9.2 + - - +
194A VAL* 3.1 29.5 + - - +
164B LYS* 3.4 14.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A LEU* 3.7 18.3 - - + +
173A LEU* 3.7 36.9 - - + +
177A LYS* 4.4 15.0 - - + -
185A GLY 4.8 0.6 + - - -
186A TYR* 4.9 7.6 - - + -
187A SER 2.9 15.7 + - - +
188A LEU 3.8 3.4 - - - +
190A GLU* 1.3 73.2 - - - +
192A VAL* 1.4 66.5 + - - +
194A VAL* 3.1 12.5 + - - +
195A ILE 3.4 7.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A GLU* 5.4 5.4 - - + +
98A VAL* 3.9 13.9 - - + -
99A GLY* 4.3 13.5 - - - +
102A LEU* 3.9 18.6 - - + -
188A LEU* 3.0 31.7 + - + +
189A GLU* 3.8 6.7 - - - +
191A ALA* 1.4 74.2 - - - +
193A ALA* 1.3 63.1 + - - +
195A ILE* 3.1 5.9 + - - +
196A PHE* 3.1 46.2 + - + -
304A EDO 4.0 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A GLU* 3.0 9.6 + - + +
190A GLU* 3.4 12.1 - - - +
191A ALA 3.2 0.2 - - - -
192A VAL* 1.3 73.7 - - - +
194A VAL* 1.3 65.3 + - - +
196A PHE* 3.5 1.7 + - - +
197A ALA* 2.9 23.6 + - - +
304A EDO 3.2 36.0 + - - +
161B VAL* 4.4 9.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A LEU* 3.9 27.6 - - + -
190A GLU 3.1 18.8 + - - +
191A ALA 3.1 8.2 + - - +
193A ALA* 1.3 75.1 - - - +
195A ILE* 1.3 59.2 + - - +
197A ALA* 3.1 2.4 + - - +
198A ASN* 2.8 42.8 + - - +
161B VAL* 4.2 17.5 - - + +
164B LYS* 3.6 37.5 - - + +
165B ALA* 3.9 22.9 - - + -
168B SER* 4.8 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A THR* 5.1 0.9 - - + -
98A VAL* 3.7 38.8 - - + -
102A LEU* 4.5 0.4 - - + -
166A PHE* 3.8 14.6 - - + +
169A ALA* 3.4 33.0 - - + -
170A ILE* 3.9 20.4 - - + +
173A LEU* 3.6 19.3 - - + -
191A ALA 3.4 2.8 + - - +
192A VAL 3.1 7.6 + - - +
194A VAL* 1.3 76.7 - - - +
196A PHE* 1.4 64.4 + - + +
198A ASN* 3.0 8.7 + - + +
199A LEU* 3.0 43.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A GLY 4.0 5.4 - - - -
94A THR* 3.8 26.9 - - + -
95A GLU* 3.6 48.0 - - + -
98A VAL* 4.9 3.6 - - + -
192A VAL* 3.1 42.0 + - + -
193A ALA 3.9 0.4 - - - +
194A VAL 3.3 0.2 - - - -
195A ILE* 1.4 77.7 - - + +
197A ALA* 1.3 55.1 + - - +
199A LEU* 3.4 2.4 + - - +
200A GLN* 2.9 29.9 + - - +
201A ILE* 4.3 19.3 + - + -
206A ARG* 4.8 15.9 - - - -
304A EDO 3.5 32.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ALA 2.9 19.7 + - - +
194A VAL 3.6 2.7 - - - +
196A PHE* 1.3 72.0 - - - +
198A ASN* 1.3 65.6 + - - +
200A GLN* 3.2 23.7 + - - +
157B ALA* 3.8 19.5 - - + -
161B VAL* 3.6 25.6 - - + -
162B GLU* 5.5 6.2 - - - +
165B ALA* 6.0 0.2 - - + -
198B ASN 3.7 3.6 - - - +
200B GLN* 3.4 10.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ARG* 2.8 28.6 + - - -
165A ALA 5.9 0.4 - - - +
166A PHE* 6.6 0.2 - - - -
169A ALA* 3.5 27.7 - - - +
194A VAL* 2.8 27.3 + - - +
195A ILE* 3.0 11.4 + - + +
197A ALA* 1.3 76.4 - - - +
199A LEU* 1.3 60.9 + - + +
162B GLU* 5.4 0.2 + - - -
165B ALA* 3.2 32.2 - - - +
197B ALA 3.8 1.4 - - - +
198B ASN* 3.5 37.6 + - - +
200B GLN* 3.0 5.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A THR* 3.8 23.8 - - + -
144A LEU* 4.4 18.8 - - + -
145A ILE* 4.8 7.4 - - + -
148A LEU* 4.1 17.9 - - + -
153A TRP* 2.7 36.9 + - + +
156A ARG* 3.1 14.6 + - - +
162A GLU* 5.2 1.8 - - - +
166A PHE* 4.8 7.4 - - + -
195A ILE* 3.0 39.0 + - + +
196A PHE* 4.1 3.4 - - - +
198A ASN* 1.3 81.0 - - + +
200A GLN* 1.3 63.5 + - - +
201A ILE* 3.4 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A TRP* 4.0 2.4 + - - -
156A ARG* 4.5 0.7 - - - +
196A PHE 2.9 15.4 + - - +
197A ALA* 3.2 28.2 + - - +
198A ASN 3.5 0.2 - - - -
199A LEU* 1.3 79.0 - - - +
201A ILE* 1.3 58.9 + - - +
202A PRO* 3.3 11.4 - - - +
206A ARG* 5.9 1.2 + - - -
156B ARG* 3.7 35.2 + - + +
157B ALA* 4.5 2.8 - - - +
162B GLU* 5.7 0.2 + - - -
200B GLN* 3.9 25.5 + - + +
----------------------------------------------------------
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