Contacts of the helix formed by residues 174 - 187 (chain A) in PDB entry 3K3T
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 PRO 174 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ALA* 3.7 4.4 - - - +
173A VAL* 1.3 88.7 - - + +
175A ALA* 1.3 66.6 + - - +
176A HIS* 3.6 26.2 - - + +
177A PHE* 3.1 42.0 + - + +
178A LEU 4.1 0.3 + - - -
266A LYS 3.4 16.6 - - - +
267A THR* 4.2 16.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A TRP* 3.6 29.8 - - + -
164A ALA* 3.8 2.1 - - + +
165A ALA* 3.7 31.6 - - + +
168A ALA* 3.6 12.3 - - + +
169A GLN* 6.4 0.7 - - + -
173A VAL 3.6 2.6 + - - -
174A PRO* 1.3 71.8 - - - +
176A HIS* 1.3 62.7 + - - +
178A LEU* 3.1 17.3 + - - +
179A VAL* 3.3 12.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A TRP* 4.1 6.0 - - + -
174A PRO* 3.6 16.2 - - + +
175A ALA* 1.3 75.5 + - - +
177A PHE* 1.3 88.6 + + - +
179A VAL* 3.8 9.1 - - - +
180A ALA* 2.9 31.5 + - - +
295A ILE* 3.6 27.1 + - + +
296A ASN* 5.5 1.4 + - - -
300A LEU* 3.8 11.3 - - + +
304A LEU* 3.5 34.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A VAL* 4.3 1.6 - - + -
174A PRO* 3.1 29.1 + - + +
175A ALA 3.1 0.4 - - - -
176A HIS* 1.3 109.6 - + - +
178A LEU* 1.3 60.5 + - + +
180A ALA* 3.5 3.1 + - - +
181A GLN* 3.1 26.2 + - - +
266A LYS 3.7 17.9 - - - -
267A THR 3.4 22.9 - - - -
268A ASP 3.6 17.9 - - - -
269A GLY 3.4 13.2 - - - -
272A PHE* 3.5 44.6 - + + -
295A ILE* 3.5 26.6 - - + +
296A ASN* 5.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ALA* 3.7 19.7 - - + +
167A ALA* 3.6 31.6 - - + -
168A ALA* 3.7 8.7 - - + +
171A LEU* 4.5 1.8 - - + -
173A VAL* 3.5 31.6 - - + -
174A PRO 4.3 0.2 - - - +
175A ALA 3.1 8.6 + - - +
177A PHE* 1.3 79.8 - - - +
179A VAL* 1.3 65.8 + - - +
181A GLN* 3.3 7.6 + - - +
182A ALA* 3.0 24.1 + - - +
205A PHE* 3.7 4.8 - - + -
247A PHE* 4.2 11.7 - - + -
250A TYR* 3.7 37.2 - - + +
272A PHE* 4.1 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A PHE* 4.6 4.6 - - + -
157A VAL* 4.3 21.5 - - + +
160A THR* 4.1 21.5 - - - +
161A TRP* 4.1 23.1 - - + -
164A ALA* 3.6 24.2 - - + -
175A ALA 3.3 7.4 + - - +
176A HIS* 3.4 9.8 + - - +
178A LEU* 1.3 76.7 - - - +
180A ALA* 1.3 56.9 + - - +
182A ALA* 3.3 6.5 + - - +
183A ALA* 2.8 27.9 + - - +
188A TRP* 5.3 1.6 - - + -
247A PHE* 5.7 0.4 - - - -
300A LEU* 4.0 19.7 - - + -
304A LEU* 4.9 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A HIS 2.9 18.3 + - - +
177A PHE 3.6 0.7 - - - +
179A VAL* 1.3 75.3 - - - +
181A GLN* 1.3 57.9 + - - +
183A ALA* 3.2 4.7 + - - +
184A LEU* 2.9 30.8 + - - +
291A LEU* 3.8 3.1 - - + -
294A VAL* 3.7 25.5 - - + +
295A ILE* 3.4 29.2 - - + +
300A LEU* 3.8 12.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A PHE 3.1 16.5 + - - +
178A LEU* 3.6 6.3 - - - +
179A VAL 3.3 0.2 - - - -
180A ALA* 1.3 77.0 - - - +
182A ALA* 1.3 57.6 + - - +
184A LEU* 3.5 2.8 + - - +
185A ALA* 3.0 27.4 + - - +
205A PHE* 3.7 13.8 - - + -
250A TYR* 2.7 35.3 + - - -
272A PHE* 3.7 4.3 - - + -
276A LEU* 3.5 25.5 - - + +
281A TYR* 3.4 39.9 - - + -
287A TYR* 3.5 15.8 + - - +
291A LEU* 3.5 15.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A PHE* 3.9 7.2 - - + -
160A THR* 5.4 0.7 - - + -
178A LEU 3.0 16.3 + - - +
179A VAL* 3.6 6.3 - - - +
181A GLN* 1.3 72.8 - - - +
183A ALA* 1.3 65.3 + - - +
185A ALA* 3.3 0.9 + - - +
186A THR* 2.8 33.1 + - - +
204A LEU* 3.5 44.0 - - + -
205A PHE* 3.7 10.0 - - + -
247A PHE* 4.9 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A PHE* 3.9 9.6 - - + -
179A VAL* 2.8 17.0 + - + +
180A ALA* 3.2 8.7 + - - +
182A ALA* 1.3 77.1 - - - +
184A LEU* 1.3 56.5 + - - +
187A GLY* 2.8 13.5 + - - -
188A TRP* 2.8 74.7 + - + +
294A VAL* 4.5 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A ALA 2.9 16.1 + - - +
181A GLN 3.8 4.3 - - - +
183A ALA* 1.3 76.4 - - - +
185A ALA* 1.3 63.3 + - - +
186A THR 3.4 0.5 + - - -
187A GLY* 3.8 5.1 + - - -
287A TYR* 3.8 28.3 - - + -
290A LYS* 4.1 20.9 - - + -
291A LEU* 3.8 35.4 - - + +
294A VAL* 4.5 18.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A GLN 3.0 17.3 + - - +
182A ALA 3.3 0.6 + - - +
184A LEU* 1.3 77.0 - - - +
186A THR* 1.3 57.2 + - - +
191A SER* 4.4 2.8 - - - +
204A LEU 3.4 21.8 - - - +
205A PHE* 4.3 0.4 - - - -
206A ASN* 2.9 31.9 + - - +
281A TYR* 3.8 19.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A PHE* 3.5 7.4 - - - -
182A ALA 2.8 14.5 + - - +
185A ALA* 1.3 78.8 - - + +
187A GLY* 1.3 61.2 + - - +
188A TRP 3.7 0.9 + - - -
189A GLY 2.9 18.7 + - - -
190A LYS 3.2 1.6 + - - -
191A SER* 2.8 51.3 + - - +
192A GLN* 3.9 17.3 - - + -
203A ASN 4.9 0.4 - - - +
204A LEU* 3.2 40.2 - - + +
206A ASN* 4.7 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A ALA 2.8 9.6 + - - -
184A LEU 3.8 4.1 + - - -
185A ALA 3.7 1.4 - - - -
186A THR* 1.3 76.7 - - - +
188A TRP* 1.3 67.6 + - - -
190A LYS* 2.8 41.5 + - - +
191A SER* 5.0 2.0 - - - -
----------------------------------------------------------
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