Contacts of the helix formed by residues 201 - 205 (chain Q) in PDB entry 3K9Q
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 ALA 201 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49P THR* 4.1 14.6 - - + -
180P TYR* 4.9 0.7 - - - +
238P ALA* 5.4 0.9 - - + -
185Q ASN 3.9 0.9 - - - -
186Q THR 3.5 21.1 - - - +
187Q GLN* 4.1 12.3 - - - +
188Q ASP* 2.8 21.2 + - - +
200Q ARG* 1.3 66.8 - - - +
202Q ALA* 1.3 66.3 + - - +
203Q ALA 3.3 1.6 + - - -
204Q GLU* 3.4 17.9 + - + -
205Q ASN* 2.9 32.1 + - - +
207Q ILE* 3.9 0.7 - - - +
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Residues in contact with ALA 202 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186P THR* 3.9 19.1 - - + -
180Q TYR* 3.9 20.1 - - + +
184Q GLN* 3.7 35.1 + - + +
185Q ASN 3.0 17.9 + - - +
186Q THR* 4.0 2.5 + - - -
200Q ARG 2.8 6.7 + - - -
201Q ALA* 1.3 73.3 - - - +
203Q ALA* 1.3 59.0 + - + +
204Q GLU 3.2 2.1 + - - -
205Q ASN 4.0 11.6 - - - +
207Q ILE* 4.4 2.0 - - - +
234Q ARG 5.4 0.5 - - - +
235Q VAL 4.7 0.7 - - - -
236Q PRO* 4.2 3.3 - - - +
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Residues in contact with ALA 203 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180P TYR* 4.0 11.1 + - + +
203P ALA* 3.4 33.7 - - + -
204P GLU* 4.9 1.8 - - - +
180Q TYR* 4.0 19.5 - - + +
186Q THR 5.0 0.6 + - - -
201Q ALA* 3.3 1.0 - - - +
202Q ALA* 1.3 78.6 - - + +
204Q GLU* 1.3 69.5 + - - +
236Q PRO* 3.3 24.9 - - + +
236R PRO 4.7 1.7 - - - +
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Residues in contact with GLU 204 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204O GLU* 3.6 20.4 - - - +
49P THR* 3.7 21.0 - - + +
50P MET* 4.6 8.7 - - - +
180P TYR* 2.9 36.2 + - - +
203P ALA* 4.9 1.4 - - - +
236P PRO 4.6 6.1 - - - +
237P VAL* 5.6 0.4 - - - -
238P ALA* 3.6 24.7 + - + +
201Q ALA* 3.4 10.7 + - + -
202Q ALA 3.2 1.0 - - - -
203Q ALA* 1.3 88.6 - - - +
205Q ASN* 1.3 69.1 + - - +
236Q PRO* 4.3 0.4 - - - -
236R PRO 5.7 0.4 - - - -
237R VAL* 3.8 14.2 - - - +
280R SER* 4.4 1.0 + - - -
281R SER* 4.5 3.6 - - - -
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Residues in contact with ASN 205 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49P THR* 3.2 20.7 + - - +
200Q ARG* 4.0 2.1 - - - +
201Q ALA 2.9 23.0 + - - +
202Q ALA 4.0 4.5 + - - +
203Q ALA 3.7 0.6 - - - -
204Q GLU* 1.3 79.5 + - - +
206Q ILE* 1.3 60.5 + - - +
207Q ILE* 3.5 22.2 - - + +
234Q ARG 3.4 8.1 - - - +
235Q VAL* 3.9 0.3 - - - -
236Q PRO* 3.3 18.0 - - - +
237R VAL* 3.8 7.4 - - - -
279R VAL* 3.2 15.2 - - + +
280R SER* 3.4 3.4 - - - +
281R SER* 2.5 51.7 + - - +
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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