Contacts of the helix formed by residues 234 - 245 (chain P) in PDB entry 3QUM
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 TYR 234 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91P HIS* 3.8 26.0 - + - -
100P SER 4.2 1.0 + - - -
101P HIS* 2.9 50.0 + + + -
103P LEU* 3.7 27.1 - - + -
179P PHE* 3.2 26.6 + + + +
229P THR* 3.8 16.5 - - + +
230P LYS 3.3 23.3 - - - -
231P VAL* 2.4 29.3 + - - +
233P HIS* 1.3 81.1 - + + +
235P ARG* 1.3 63.6 - - - +
236P LYS 3.4 2.0 - - - -
237P TRP* 3.1 18.7 + - + +
238P ILE* 3.3 15.6 + - + +
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Residues in contact with ARG 235 (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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1F A2G 5.1 0.6 - - - -
123P LEU* 3.4 41.3 + - + +
124P PRO* 3.2 19.8 + - + +
125P THR* 3.0 31.9 - - - +
231P VAL* 3.5 4.1 + - - -
232P VAL* 3.8 14.6 - - - +
233P HIS 3.5 2.8 - - - -
234P TYR* 1.3 78.3 - - - +
236P LYS* 1.3 66.5 + - - +
238P ILE* 3.1 9.8 + - - +
239P LYS* 2.8 51.9 + - + +
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Residues in contact with LYS 236 (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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233P HIS 5.4 0.2 + - - -
234P TYR 3.4 0.4 - - - -
235P ARG* 1.3 80.0 - - - +
237P TRP* 1.3 62.5 + - - +
239P LYS* 4.3 14.8 - - + +
240P ASP* 3.0 49.7 + - - +
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Residues in contact with TRP 237 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89P PHE* 3.8 22.2 - - + -
90P PRO 3.8 4.7 - - - -
91P HIS* 3.6 38.4 - + - +
92P PRO* 3.7 32.6 - - + +
103P LEU* 4.0 28.9 - - + -
105P LEU* 3.4 25.8 - - + -
234P TYR* 3.1 15.7 + - + +
236P LYS* 1.3 76.5 - - - +
238P ILE* 1.3 68.3 + - + +
240P ASP* 3.8 2.0 - - - +
241P THR* 2.4 60.6 + - + +
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Residues in contact with ILE 238 (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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47P VAL* 5.3 4.0 - - + -
53P LEU* 4.2 26.7 - - + -
103P LEU* 4.8 6.5 - - + -
105P LEU* 3.9 20.0 - - + -
123P LEU* 4.0 31.9 - - + -
231P VAL* 4.4 13.0 - - + -
234P TYR* 3.4 17.5 - - + +
235P ARG* 3.5 3.8 - - - +
237P TRP* 1.3 84.0 - - + +
239P LYS* 1.3 70.3 + - - +
240P ASP 2.8 3.0 + - - -
241P THR* 3.4 8.3 - - - -
242P ILE* 2.9 41.3 + - + +
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Residues in contact with LYS 239 (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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122P ASP* 6.2 1.0 - - - +
123P LEU* 4.0 30.8 - - + +
235P ARG* 2.8 57.5 + - + +
236P LYS* 3.8 17.9 - - + +
238P ILE* 1.3 75.0 - - - +
240P ASP* 1.3 65.0 + - - +
242P ILE* 3.4 7.9 - - + +
243P VAL* 3.2 26.8 + - + +
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Residues in contact with ASP 240 (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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236P LYS* 3.0 54.7 + - - +
237P TRP* 3.9 2.2 - - - +
238P ILE 2.8 0.8 + - - -
239P LYS* 1.3 77.9 - - - +
241P THR* 1.3 67.6 + - - +
242P ILE 2.9 1.6 - - - -
243P VAL* 2.8 23.6 + - - +
244P ALA* 3.0 14.5 + - - +
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Residues in contact with THR 241 (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 TRP* 4.9 3.2 - - - -
89P PHE* 4.4 18.9 - - - +
105P LEU* 3.8 15.1 - - + +
237P TRP* 2.4 75.4 + - + +
238P ILE* 3.4 11.9 - - - -
240P ASP* 1.3 73.0 - - - +
242P ILE* 1.3 59.8 + - - +
244P ALA* 5.0 2.2 - - - -
245P ASN* 3.3 30.1 + - - +
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Residues in contact with ILE 242 (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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47P VAL* 4.3 11.4 - - + +
48P HIS* 4.5 15.5 - - + +
51P TRP* 3.7 65.2 + - + +
105P LEU* 4.6 6.5 - - + -
123P LEU* 6.2 0.9 - - + -
238P ILE* 2.9 33.7 + - + +
239P LYS* 3.4 11.9 - - + +
240P ASP 2.9 0.2 - - - -
241P THR* 1.3 76.9 - - - +
243P VAL* 1.3 72.8 + - + +
244P ALA 3.4 0.3 + - - -
245P ASN 3.5 9.9 + - - -
246P PRO* 4.3 2.3 - - - +
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Residues in contact with VAL 243 (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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239P LYS* 3.2 17.3 - - + +
240P ASP* 2.8 18.7 + - - +
242P ILE* 1.3 82.7 - - + +
244P ALA* 1.3 65.6 + - + +
246P PRO* 3.4 18.2 - - - +
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Residues in contact with ALA 244 (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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240P ASP 3.0 13.2 + - - +
241P THR* 3.7 2.2 + - - +
242P ILE 3.3 0.2 - - - -
243P VAL* 1.3 78.1 - - + +
245P ASN* 1.3 74.5 + - - +
246P PRO* 3.2 11.5 - - - +
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Residues in contact with ASN 245 (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 TRP* 3.6 8.4 - - + -
87P HIS* 5.8 0.2 - - - -
89P PHE* 3.5 39.7 - - + -
107P ARG* 2.6 31.8 + - - +
241P THR* 3.3 20.9 + - - +
242P ILE 3.5 8.1 + - - -
243P VAL 3.3 1.4 - - - -
244P ALA* 1.3 91.4 - - - +
246P PRO* 1.4 60.2 - - - +
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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