Contacts of the helix formed by residues 173 - 183 (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 HIS 173 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27P LEU* 3.5 42.8 + - + +
29P LEU* 4.5 12.7 - - + +
33P PHE 5.1 2.4 + - - -
35P LEU* 3.2 39.2 - - + +
47P LEU* 5.2 7.0 - - + -
172P LEU* 1.3 72.9 - - - +
174P PRO* 1.4 76.8 - - + +
175P PHE* 2.5 53.6 + - + +
176P GLU* 3.0 11.8 + - - +
177P VAL* 2.9 21.1 + - - +
201P LYS* 3.7 10.2 - - - +
3S PHE* 6.5 0.4 - + - -
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Residues in contact with PRO 174 (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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35P LEU* 3.7 17.5 - - + -
46P GLU* 3.3 37.0 - - + +
47P LEU* 3.7 28.0 - - + +
49P ALA* 3.4 18.6 - - + +
168P LYS* 4.3 11.8 + - - +
172P LEU 3.8 1.9 - - - +
173P HIS* 1.4 93.7 - - + +
175P PHE* 1.3 56.4 + - - +
177P VAL* 3.8 7.7 - - + +
178P ALA* 2.9 27.4 + - - +
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Residues in contact with PHE 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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27P LEU* 4.0 21.3 - - + -
29P LEU* 5.1 10.8 - - + -
49P ALA* 4.2 4.0 - - + +
173P HIS* 2.5 38.9 + - + +
174P PRO* 1.3 70.0 - - - +
176P GLU* 1.3 58.3 + - + +
178P ALA* 2.9 6.6 + - - +
179P GLN* 2.7 59.2 + - + +
195P ILE* 5.8 1.8 - - + -
197P SER* 5.2 2.9 - - - -
1S MET* 3.2 41.3 - - + -
3S PHE* 4.5 11.9 - + + -
82S PHE* 4.7 11.7 - + + -
85S GLU* 4.2 28.3 - - + -
86S VAL 5.9 0.4 - - - -
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Residues in contact with GLU 176 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27P LEU* 3.7 13.2 - - + -
172P LEU* 3.1 21.5 - - + +
173P HIS* 3.0 25.7 + - - +
175P PHE* 1.3 79.7 - - + +
177P VAL* 1.3 57.6 - - - +
179P GLN* 2.8 4.4 + - - +
180P LEU* 2.8 36.0 + - - +
195P ILE* 3.9 8.3 - - + -
197P SER* 2.7 58.7 - - - +
198P LEU* 3.0 18.7 + - + -
201P LYS* 3.2 11.9 + - - +
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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
----------------------------------------------------------
51P ASN* 4.9 2.3 + - - +
164P ILE* 6.0 0.4 - - - -
167P LEU* 3.5 37.9 - - + +
168P LYS* 3.6 35.4 - - + +
170P THR* 4.1 7.9 - - - +
172P LEU* 3.5 34.7 - - + +
173P HIS 2.9 20.4 + - - +
174P PRO 3.8 4.9 - - - +
176P GLU* 1.3 75.5 - - - +
178P ALA* 1.3 63.0 + - - +
180P LEU* 4.2 3.4 - - - +
181P GLY* 3.4 13.5 + - - -
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Residues in contact with ALA 178 (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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49P ALA* 3.8 13.0 - - + -
50P LEU 4.3 0.4 - - - +
51P ASN* 3.1 41.9 - - - +
174P PRO 2.9 16.2 + - - +
175P PHE 2.9 13.5 - - - +
177P VAL* 1.3 77.9 - - - +
179P GLN* 1.3 60.6 + - - +
181P GLY 3.2 1.4 + - - -
182P SER* 3.1 8.9 + - - -
1S MET 3.5 22.9 - - - +
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Residues in contact with GLN 179 (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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52P LEU* 6.2 0.4 - - - +
175P PHE* 2.7 42.4 + - + +
176P GLU* 2.8 8.9 + - - +
178P ALA* 1.3 69.2 - - - +
180P LEU* 1.3 66.5 + - - +
181P GLY 3.0 1.3 - - - -
182P SER* 2.9 13.2 + - - -
183P LEU* 2.8 40.4 + - - +
194P LEU 6.0 0.4 - - - +
195P ILE* 4.0 23.3 - - + -
1S MET* 3.6 34.8 - - - +
85S GLU* 4.5 3.4 + - + -
86S VAL* 3.4 24.5 + - + +
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Residues in contact with LEU 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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153P ARG* 3.8 6.1 + - - -
167P LEU* 5.1 9.4 - - + -
172P LEU* 4.3 15.7 - - + -
176P GLU 2.8 16.9 + - - +
177P VAL* 4.5 4.7 - - - +
179P GLN* 1.3 71.1 - - - +
181P GLY* 1.3 62.4 + - - +
183P LEU 3.6 15.1 - - - +
185P CYS* 4.6 12.1 - - + -
191P ALA* 4.2 16.4 - - + -
195P ILE* 3.6 21.1 - - + -
198P LEU* 3.8 33.7 - - + -
202P ILE* 6.2 0.2 - - + -
207P LEU* 4.3 19.1 - - + -
210P ILE* 6.5 0.7 - - + -
211P LEU* 4.9 6.3 - - + -
214P LEU* 4.5 7.6 - - - +
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Residues in contact with GLY 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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51P ASN* 4.0 14.7 - - - +
153P ARG* 3.7 18.9 + - - +
154P PHE* 4.3 11.1 - - - -
163P VAL* 4.7 6.1 - - - -
167P LEU* 4.2 14.3 - - - +
177P VAL 3.4 10.6 + - - -
178P ALA 3.2 7.9 + - - -
179P GLN 3.0 1.0 - - - -
180P LEU* 1.3 81.9 - - - +
182P SER* 1.3 59.0 + - - +
214P LEU* 4.9 2.7 - - - -
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Residues in contact with SER 182 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51P ASN* 3.8 3.6 - - - +
52P LEU* 3.4 53.3 + - - +
151P PHE 5.1 5.4 - - - +
153P ARG* 4.5 12.7 - - - +
178P ALA 3.1 13.6 + - - -
179P GLN* 2.9 19.3 + - - -
181P GLY* 1.3 75.6 - - - +
183P LEU* 1.3 69.2 + - - +
184P ALA 4.2 0.9 + - - -
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Residues in contact with LEU 183 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52P LEU* 6.4 0.2 - - + -
153P ARG* 3.5 9.0 + - - -
179P GLN* 2.8 28.9 + - - +
180P LEU* 3.6 10.9 - - - +
181P GLY 3.5 1.4 - - - -
182P SER* 1.3 80.5 - - - +
184P ALA* 1.3 69.0 - - - +
185P CYS* 3.0 14.0 + - - +
194P LEU* 4.8 7.2 - - + -
195P ILE* 5.4 8.3 - - + -
86S VAL* 3.8 43.5 - - + +
87S VAL* 4.6 5.8 - - - -
88S ASP* 4.2 11.4 - - - +
144S ARG* 3.6 36.8 - - - +
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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