Contacts of the helix formed by residues 156 - 168 (chain P) in PDB entry 3HOU
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 ASP 156 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57P LEU* 4.4 0.2 - - - -
154P PHE 3.6 0.8 - - - -
155P ARG* 1.3 88.7 + - - +
157P GLN* 1.3 56.6 + - - +
158P GLU* 2.6 33.7 + - - +
159P THR* 2.9 35.6 + - + +
160P VAL* 2.9 10.8 - - - +
219P THR* 2.6 32.4 + - - +
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Residues in contact with GLN 157 (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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57P LEU* 3.0 42.5 - - + +
156P ASP* 1.3 70.2 - - - +
158P GLU* 1.3 69.5 + - - +
160P VAL* 3.9 9.5 - - - +
161P GLY* 3.4 14.9 + - - +
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Residues in contact with GLU 158 (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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156P ASP* 2.6 31.0 + - - +
157P GLN* 1.3 84.4 + - - +
159P THR* 1.3 58.1 + - + +
160P VAL 3.0 0.9 - - - -
161P GLY* 2.7 23.0 + - - -
162P ALA* 2.8 13.1 + - - +
165P GLN* 5.2 0.5 + - - -
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Residues in contact with THR 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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154P PHE* 3.3 18.9 - - - +
156P ASP* 2.9 38.1 + - + +
158P GLU* 1.3 73.7 - - + +
160P VAL* 1.3 60.2 + - - +
162P ALA* 3.1 10.5 + - - +
163P VAL* 2.6 40.1 + - - +
217P LEU* 4.0 17.0 - - - +
219P THR* 3.1 19.8 + - - +
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Residues in contact with VAL 160 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51P ASN* 5.1 3.1 - - - +
53P SER* 4.8 3.4 - - - +
54P GLU* 3.8 36.8 - - + +
57P LEU* 4.0 17.5 - - + -
154P PHE* 3.9 18.6 - - + +
156P ASP 2.9 24.5 - - - +
157P GLN* 3.9 12.6 - - - +
159P THR* 1.3 77.2 - - - +
161P GLY* 1.3 64.9 + - - +
163P VAL* 3.3 10.4 - - + +
164P ILE* 2.8 40.6 + - + +
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Residues in contact with GLY 161 (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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157P GLN* 3.4 9.3 + - - +
158P GLU* 2.7 15.3 + - - -
160P VAL* 1.3 73.7 - - - +
162P ALA* 1.3 61.9 + - - -
164P ILE* 2.9 15.3 + - - +
165P GLN* 2.8 34.6 + - - +
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Residues in contact with ALA 162 (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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158P GLU 2.8 10.1 + - - +
159P THR* 3.1 14.1 - - - +
161P GLY* 1.3 75.3 - - - +
163P VAL* 1.3 65.2 + - - +
165P GLN* 3.2 18.3 + - - +
166P LEU* 2.9 24.9 + - - +
217P LEU* 3.2 27.7 - - + +
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Residues in contact with VAL 163 (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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51P ASN* 4.8 7.9 - - - +
154P PHE* 2.9 47.8 - - + -
159P THR 2.6 28.4 + - - +
160P VAL* 3.3 7.6 - - + +
162P ALA* 1.3 71.9 - - - +
164P ILE* 1.3 65.1 + - + +
166P LEU* 2.9 28.8 - - - +
167P LEU* 2.9 24.8 - - + +
181P GLY* 4.7 5.2 - - - -
214P LEU* 3.5 17.9 - - + -
217P LEU* 4.6 7.9 - - + -
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Residues in contact with ILE 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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51P ASN* 5.1 2.5 - - - +
54P GLU* 3.8 37.0 - - + +
157P GLN* 6.2 1.6 - - - +
160P VAL* 2.8 33.7 - - + +
161P GLY* 2.9 11.6 + - - +
163P VAL* 1.3 76.3 - - + +
165P GLN* 1.3 53.1 + - + +
167P LEU* 3.9 5.7 - - - +
168P LYS* 2.8 66.1 + - + +
177P VAL* 6.0 0.4 - - - -
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Residues in contact with GLN 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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158P GLU 5.2 0.2 + - - -
161P GLY* 2.8 13.0 + - - +
162P ALA* 3.4 29.2 - - - +
164P ILE* 1.3 75.4 - - + +
166P LEU* 1.3 67.1 + - - +
168P LYS* 3.3 17.7 + - - +
169P SER* 3.9 5.4 + - - -
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Residues in contact with LEU 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 ALA 2.9 9.8 + - - +
163P VAL* 2.9 13.0 - - - +
165P GLN* 1.3 74.8 - - - +
167P LEU* 1.3 61.3 - - + +
169P SER* 2.6 27.2 + - - -
170P THR* 4.4 2.9 - - - +
210P ILE* 4.2 19.9 - - + +
213P GLU* 3.7 38.1 - - + +
214P LEU* 4.1 25.1 - - + +
217P LEU* 3.5 29.2 - - + -
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Residues in contact with LEU 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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51P ASN* 5.4 2.9 - - - +
163P VAL* 2.9 35.6 + - + +
164P ILE* 4.1 3.6 - - - +
166P LEU* 1.3 90.3 - - + +
168P LYS* 1.3 54.6 + - - +
169P SER 2.6 18.9 + - - -
170P THR* 2.8 34.7 + - + +
172P LEU* 5.8 1.8 - - + -
177P VAL* 3.5 42.6 - - + +
180P LEU* 5.1 7.0 - - + -
181P GLY* 4.2 13.5 - - - +
210P ILE* 3.8 17.7 - - + -
214P LEU* 4.3 7.4 - - + -
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Residues in contact with LYS 168 (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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46P GLU* 4.7 9.9 + - - +
49P ALA 5.6 4.2 + - - -
164P ILE* 2.8 51.8 + - + +
165P GLN* 3.3 9.9 + - - +
167P LEU* 1.3 67.4 - - - +
169P SER* 1.3 57.3 + - - +
170P THR 3.7 0.2 - - - -
171P GLY 5.0 2.2 - - - +
174P PRO* 4.3 14.6 + - - +
177P VAL* 3.6 36.9 - - + +
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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
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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