Contacts of the helix formed by residues 152 - 168 (chain P) in PDB entry 2QJK
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 152 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77P PHE* 4.5 2.2 - - - -
150P PRO 3.4 3.4 - - - -
151P TRP* 1.3 75.3 - - - +
153P GLN* 1.3 67.3 + - - -
155P SER* 3.1 8.1 + - - -
156P PHE 2.9 18.2 + - - -
279P ASN* 3.1 20.6 - - - -
281P ILE 3.2 14.1 - - - -
282P GLU* 4.3 0.4 - - - -
283P ALA* 3.3 12.2 - - - +
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Residues in contact with GLN 153 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152P GLY* 1.3 69.6 - - - +
154P MET* 1.3 73.3 + - + +
155P SER 2.9 1.4 + - - -
156P PHE* 3.1 7.8 + - - +
157P TRP* 3.2 30.0 + - - -
278P ASP 3.2 12.5 + - - +
279P ASN* 3.2 2.2 + - - -
281P ILE* 2.9 41.2 + - + +
282P GLU 3.8 2.7 - - - +
283P ALA* 3.6 0.5 - - - +
284P ASN* 2.8 39.5 + - - +
287P ARG* 3.3 29.3 + - - +
289P PRO* 3.4 31.4 - - + +
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Residues in contact with MET 154 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147P TYR* 3.4 34.4 - - + +
153P GLN* 1.3 74.9 - - - +
155P SER* 1.3 57.7 + - - +
157P TRP* 5.2 0.7 - - - -
158P GLY* 2.9 29.8 + - - +
276P HIS* 3.6 42.8 - - + +
278P ASP* 3.6 22.6 + - + +
279P ASN* 3.0 12.0 + - - +
289P PRO* 3.7 27.1 - - + -
292P ILE* 3.9 28.0 - - + -
293P VAL 4.0 8.1 - - - +
503P SMA 4.2 8.0 - - - +
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Residues in contact with SER 155 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147P TYR* 2.6 27.0 + - - -
148P VAL* 3.3 29.9 + - - +
150P PRO* 4.2 1.2 - - - +
151P TRP* 3.7 3.3 + - - -
152P GLY 3.2 23.4 + - - -
153P GLN 2.9 0.6 - - - -
154P MET* 1.3 78.6 - - - +
156P PHE* 1.3 65.6 + - - +
158P GLY* 4.1 0.2 - - - -
159P ALA* 3.2 20.3 + - - +
279P ASN* 3.0 19.7 + - - +
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Residues in contact with PHE 156 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69O GLY 5.0 5.4 - - - -
151P TRP* 3.9 25.3 - + + -
152P GLY 2.9 13.9 + - - +
153P GLN* 3.1 3.3 + - - +
155P SER* 1.3 72.6 - - - +
157P TRP* 1.3 105.9 + + + +
159P ALA* 2.8 16.6 + - - +
160P THR* 2.9 16.2 + - - -
185P ALA* 6.2 0.4 - - + -
186P VAL* 3.2 49.8 - - + +
283P ALA* 3.8 15.7 - - + +
284P ASN 4.0 7.2 - - - -
285P PRO* 3.2 40.8 - - + -
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Residues in contact with TRP 157 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71O PRO* 5.1 4.9 - - + -
133O GLY 4.2 3.1 - - - -
134O CYS* 3.8 22.4 - - - -
135O SER* 4.0 11.2 - - - -
153P GLN* 3.2 20.6 + - - +
154P MET 4.6 0.2 - - - +
156P PHE* 1.3 90.2 - + - +
158P GLY* 1.3 66.5 + - - +
160P THR* 2.8 37.2 + - + -
161P VAL* 2.9 16.8 + - - +
284P ASN 3.3 22.9 + - - -
285P PRO 3.6 17.5 - - - -
287P ARG* 2.6 32.1 + - - -
288P THR* 3.3 23.8 - - + -
289P PRO* 3.4 22.2 - - + -
292P ILE* 3.7 20.9 - - + -
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Residues in contact with GLY 158 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144P PHE* 4.4 2.9 - - - -
147P TYR* 6.2 0.7 - - - -
154P MET* 2.9 21.4 + - - +
155P SER 4.1 0.2 - - - -
157P TRP* 1.3 77.7 - - - +
159P ALA* 1.3 56.6 + - - +
161P VAL* 3.3 2.0 + - - +
162P ILE* 2.9 37.0 + - - +
292P ILE* 4.8 1.2 - - - +
503P SMA 3.5 29.6 + - - -
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Residues in contact with ALA 159 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144P PHE* 3.8 16.2 - - + -
148P VAL* 4.0 22.7 - - + -
155P SER 3.2 13.4 + - - +
156P PHE* 2.8 10.2 + - - +
158P GLY* 1.3 72.3 - - - +
160P THR* 1.3 68.5 + - - +
162P ILE* 4.1 0.3 - - - +
163P THR* 2.8 30.4 + - + +
186P VAL* 4.1 16.6 - - + -
190P THR* 5.8 0.9 - - + -
194P PHE* 4.5 6.7 - - + -
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Residues in contact with THR 160 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132O LEU 3.4 5.6 - - - +
133O GLY* 4.0 30.7 - - - +
134O CYS 4.5 0.4 - - - +
156P PHE* 2.9 21.8 + - - -
157P TRP* 2.8 36.9 + - + -
159P ALA* 1.3 70.9 - - - +
161P VAL* 1.3 56.9 + - + +
163P THR* 2.7 15.3 + - - -
164P GLY* 3.1 8.8 + - - -
177P GLN* 4.4 1.9 + - - -
186P VAL* 3.6 25.7 - - + +
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Residues in contact with VAL 161 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132O LEU* 3.8 35.8 - - + +
134O CYS* 3.7 30.5 - - - +
152O HIS* 4.2 2.9 - - + -
157P TRP 2.9 11.8 + - - +
158P GLY 3.6 7.0 - - - +
160P THR* 1.3 76.4 - - - +
162P ILE* 1.3 64.0 + - + +
164P GLY* 2.8 15.6 + - - -
165P LEU* 3.0 15.6 + - + +
503P SMA 3.5 49.6 - - + +
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Residues in contact with ILE 162 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144P PHE* 3.5 44.0 - - + -
158P GLY 2.9 17.0 + - - +
161P VAL* 1.3 74.6 - - + +
163P THR* 1.3 66.0 + - - +
165P LEU* 3.4 15.3 + - + +
166P PHE* 3.3 18.2 - - - -
298P PHE* 4.9 1.1 - - + -
503P SMA 3.5 91.1 - - + +
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Residues in contact with THR 163 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144P PHE* 5.3 1.3 - - + -
159P ALA 2.8 16.9 + - - +
160P THR* 2.7 23.9 + - - -
162P ILE* 1.3 77.2 - - - +
164P GLY* 1.3 62.4 + - - +
166P PHE* 3.0 25.1 + - - +
167P GLY 3.6 0.9 + - - -
177P GLN* 3.3 18.9 + - - +
180P LEU* 4.4 20.4 - - + +
181P LEU* 3.5 37.0 - - + +
186P VAL* 4.8 1.1 - - + -
190P THR* 4.8 0.7 - - + -
194P PHE* 4.5 19.7 - - + -
503P SMA 5.2 2.2 - - + -
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Residues in contact with GLY 164 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132O LEU* 3.8 21.8 - - - +
160P THR 3.1 6.7 + - - -
161P VAL 2.8 10.2 + - - -
163P THR* 1.3 79.0 + - - +
165P LEU* 1.3 55.8 + - - +
166P PHE 2.9 2.2 - - - -
167P GLY* 2.5 29.6 + - - -
168P ALA 3.2 3.5 + - - -
177P GLN* 3.1 15.3 - - - -
329P LYS* 5.2 1.7 - - - -
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Residues in contact with LEU 165 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132O LEU* 3.8 31.6 - - + -
161P VAL* 3.0 10.1 + - + +
162P ILE* 3.6 26.7 - - + +
163P THR 3.3 0.4 - - - -
164P GLY* 1.3 74.2 - - - +
166P PHE* 1.3 68.9 + - + +
168P ALA* 3.1 19.3 - - - +
169P ILE* 4.1 4.2 + - - +
305P LEU* 4.0 19.7 - - + -
333P VAL* 4.1 17.3 - - + +
336P MET* 3.8 24.9 - - + -
337P PHE* 4.5 15.4 - - + -
503P SMA 4.6 18.8 - - + +
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Residues in contact with PHE 166 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162P ILE 3.3 21.5 - - - -
163P THR 3.0 8.7 + - - +
164P GLY 2.7 2.6 + - - -
165P LEU* 1.3 77.8 - - + +
167P GLY* 1.3 61.6 + - - +
168P ALA 2.9 5.2 - - - -
169P ILE* 2.9 34.5 + - + +
173P GLY* 3.3 13.0 - - - -
176P ILE* 3.7 29.8 - - + +
177P GLN* 4.8 4.5 - - - +
180P LEU* 4.1 19.5 - - + -
337P PHE* 4.6 15.3 - + - -
503P SMA 4.1 37.2 - - + -
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Residues in contact with GLY 167 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163P THR 3.6 2.6 + - - -
164P GLY 2.5 18.5 + - - -
166P PHE* 1.3 73.6 - - - +
168P ALA* 1.3 56.7 + - - -
169P ILE 3.4 6.9 + - - +
173P GLY* 3.6 16.8 - - - -
174P HIS* 4.6 2.9 + - - -
177P GLN* 3.8 19.9 - - - +
329P LYS* 4.8 8.5 + - - -
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Residues in contact with ALA 168 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132O LEU* 5.5 0.2 - - + -
164P GLY 3.2 3.5 + - - +
165P LEU* 3.1 17.0 + - - +
166P PHE 2.9 0.4 - - - -
167P GLY* 1.3 76.4 - - - +
169P ILE* 1.3 67.5 + - - +
170P PRO* 3.2 5.5 - - - +
329P LYS* 4.2 26.7 - - + +
330P PHE* 3.4 22.4 - - + +
333P VAL* 3.5 26.0 - - + -
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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) + - + + + + + -
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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