Contacts of the helix formed by residues 169 - 182 (chain P) in PDB entry 5A31
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 169 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168P ASP* 1.3 78.5 + - - +
170P PHE* 1.3 67.4 + - - -
172P LEU* 3.2 19.7 + - - +
173P TYR* 3.2 9.6 + - - +
195P ALA* 4.4 6.2 - - - +
198P VAL* 3.9 9.9 - - - +
199P LEU* 3.8 31.6 - - - -
202P HIS* 6.0 0.4 - - - -
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Residues in contact with PHE 170 (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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39P ILE* 5.1 2.5 - - + -
42P LEU* 4.0 28.7 - - + -
43P THR* 3.9 22.9 - - + -
46P ARG* 3.5 49.4 - - + -
48P LEU* 4.1 15.5 - - + -
116P PHE* 3.7 26.9 - + + -
168P ASP 3.1 3.7 + - - +
169P GLY* 1.3 71.2 - - - -
171P GLY* 1.3 56.1 + - - +
173P TYR* 2.6 30.4 + - - +
174P LEU 2.7 10.9 + - - -
199P LEU* 3.9 24.0 - - + -
202P HIS* 4.2 17.0 - + + -
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Residues in contact with GLY 171 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115P TYR* 6.3 0.2 - - - -
116P PHE* 3.8 16.3 - - - +
158P LEU* 4.8 1.8 - - - +
167P LEU* 3.4 29.0 - - - +
168P ASP 3.1 9.8 + - - -
170P PHE* 1.3 78.4 - - - +
172P LEU* 1.3 50.8 + - - +
174P LEU* 3.0 5.0 + - - +
175P TYR* 2.8 34.5 + - - +
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Residues in contact with LEU 172 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162P HIS* 4.2 22.2 - - + +
167P LEU* 3.5 41.7 - - + +
168P ASP* 4.0 7.6 - - - -
169P GLY 3.2 13.0 + - - +
170P PHE 3.1 0.2 - - - -
171P GLY* 1.3 74.1 - - - +
173P TYR* 1.3 58.1 + - - +
175P TYR* 3.2 3.3 + - - +
176P GLY* 2.8 25.3 + - - -
191P VAL* 3.4 31.6 - - + +
192P PHE* 4.9 0.2 - - - -
194P GLU* 3.7 28.0 - - + -
195P ALA* 3.8 19.2 - - + +
198P VAL* 5.3 7.0 - - + -
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Residues in contact with TYR 173 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1M MET* 3.3 28.5 + - - +
2M ASP 3.7 5.8 + - - -
48P LEU* 4.3 20.4 - - + -
116P PHE* 5.0 3.4 - + - -
120P TYR* 5.3 7.0 - + - -
169P GLY 3.2 4.4 + - - +
170P PHE* 2.6 20.9 + - - +
172P LEU* 1.3 75.5 - - - +
174P LEU* 1.3 68.4 + - + -
176P GLY* 3.1 1.9 + - - -
177P VAL* 2.9 38.2 + - + +
192P PHE* 3.7 11.9 - + - -
195P ALA* 4.2 4.6 - - + +
202P HIS* 3.6 31.4 - + + +
204P GLY* 3.5 26.6 - - - -
205P ALA* 3.6 18.2 - - + -
208P GLU* 3.2 24.9 + - + -
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Residues in contact with LEU 174 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116P PHE* 3.6 25.6 - - + -
119P MET* 4.0 25.1 - - + +
120P TYR* 3.6 37.0 - - + +
123P TYR* 4.4 14.8 - - + -
154P LEU* 4.6 2.7 - - + -
158P LEU* 3.3 32.1 - - + -
170P PHE 2.7 8.5 + - - -
171P GLY* 3.4 9.4 - - - +
173P TYR* 1.3 77.5 - - + +
175P TYR* 1.3 63.2 + - - +
177P VAL* 3.3 13.8 + - + +
178P VAL* 3.1 25.8 + - + +
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Residues in contact with TYR 175 (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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155P ARG* 4.1 29.6 + - + -
158P LEU* 3.6 25.8 - - + -
159P SER* 3.6 23.6 - - - -
162P HIS* 3.6 39.6 + + + -
167P LEU* 4.2 9.6 - - + -
171P GLY 2.8 12.6 + - - +
172P LEU* 3.4 8.5 - - + +
174P LEU* 1.3 77.5 - - - +
176P GLY* 1.3 62.1 + - - +
178P VAL* 3.0 4.4 + - + +
179P LEU* 3.0 45.7 + - + +
187P GLU* 4.9 5.6 + - - -
191P VAL* 3.8 27.6 - - + -
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Residues in contact with GLY 176 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172P LEU 2.8 14.1 + - - -
173P TYR 3.5 3.6 - - - -
175P TYR* 1.3 75.5 - - - +
177P VAL* 1.3 64.1 + - - +
179P LEU* 3.3 7.7 + - - +
180P ARG* 2.9 24.1 + - - +
188P ALA* 4.0 1.7 - - - +
191P VAL* 3.8 15.2 - - - +
192P PHE* 3.3 22.6 - - - -
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Residues in contact with VAL 177 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2M ASP* 3.3 44.0 - - + +
120P TYR* 6.2 0.2 - - + -
123P TYR* 3.6 23.3 - - + +
173P TYR* 2.9 47.3 + - + +
174P LEU* 3.3 15.7 - - + +
175P TYR 3.3 0.2 - - - -
176P GLY* 1.3 76.4 - - - +
178P VAL* 1.3 59.4 + - + +
180P ARG* 3.2 6.3 + - - +
181P LYS* 2.9 28.6 + - - +
192P PHE* 3.4 7.4 - - + -
208P GLU* 4.4 1.6 - - + -
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Residues in contact with VAL 178 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123P TYR* 3.9 17.0 - - + -
151P LEU* 3.6 46.4 - - + +
154P LEU* 4.1 12.8 - - + -
155P ARG* 4.1 24.0 - - + +
158P LEU* 4.6 2.0 - - + -
174P LEU* 3.1 19.7 + - + +
175P TYR* 3.0 11.4 + - + +
177P VAL* 1.3 73.8 - - + +
179P LEU* 1.3 67.5 + - - +
181P LYS* 3.2 5.1 + - - +
182P LEU* 3.1 24.2 + - + +
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Residues in contact with LEU 179 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473J VAL* 5.9 0.9 - - + -
155P ARG* 4.0 14.6 - - + +
175P TYR* 3.0 47.3 + - + +
176P GLY* 3.6 4.5 - - - +
178P VAL* 1.3 78.0 - - - +
180P ARG* 1.3 62.1 + - - +
182P LEU* 3.0 13.1 + - - +
184P LEU* 2.9 51.2 + - + +
187P GLU* 4.4 12.8 - - + +
188P ALA* 3.9 16.6 - - + +
191P VAL* 3.5 35.4 - - + -
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Residues in contact with ARG 180 (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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2M ASP* 2.7 30.9 + - - -
3M SER* 2.9 19.9 + - - -
176P GLY 2.9 18.2 + - - +
177P VAL* 3.5 6.0 - - - +
178P VAL 3.2 0.2 - - - -
179P LEU* 1.3 76.9 - - - +
181P LYS* 1.3 74.3 + - - +
183P ASP* 2.8 23.4 + - - +
184P LEU 4.6 2.9 - - - +
185P VAL* 5.1 4.8 - - + +
188P ALA* 4.3 9.9 - - + -
192P PHE* 4.7 2.7 - - + -
208P GLU* 2.9 33.3 + - - +
211P ASN* 5.0 9.9 - - - +
212P LEU* 3.6 40.2 - - + -
363P ARG* 3.8 22.3 - - - +
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Residues in contact with LYS 181 (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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477J GLN* 4.1 5.0 - - - +
2M ASP* 4.7 8.0 + - - -
3M SER* 4.7 7.5 + - - +
5M VAL* 6.0 1.0 - - - +
123P TYR* 3.5 23.2 + - + +
127P GLU* 3.6 26.4 + - - +
130P LYS* 5.0 8.8 - - - +
148P ASN* 5.1 0.3 - - - +
151P LEU* 3.5 22.6 - - + +
177P VAL* 2.9 17.9 + - + +
178P VAL* 3.2 5.3 + - - +
180P ARG* 1.3 100.1 - - - +
182P LEU* 1.3 61.8 + - - +
183P ASP* 3.0 12.1 - - - +
363P ARG* 4.2 27.7 - - - +
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Residues in contact with LEU 182 (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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476J PRO* 3.3 52.0 - - + +
477J GLN* 3.8 3.7 + - - -
148P ASN* 3.3 24.5 - - - +
151P LEU* 3.4 32.1 - - + -
152P ARG* 4.6 4.5 - - - +
155P ARG* 4.0 34.1 - - + -
178P VAL* 3.1 17.1 + - + +
179P LEU* 3.0 9.2 + - - +
181P LYS* 1.3 74.6 - - - +
183P ASP* 1.3 74.2 + - - +
184P LEU* 3.3 10.0 + - + +
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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
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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