Contacts of the helix formed by residues 201 - 205 (chain O) 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 O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185O ASN 3.8 1.1 - - - -
186O THR 3.4 20.9 - - - +
187O GLN* 4.1 8.3 - - - +
188O ASP* 2.8 26.8 + - - +
200O ARG* 1.3 67.5 - - - +
202O ALA* 1.3 64.6 + - - +
203O ALA 3.3 2.4 + - - +
204O GLU* 3.4 18.1 + - + -
205O ASN* 2.9 22.2 + - - +
207O ILE* 4.2 0.4 - - - +
49R THR* 4.1 18.8 - - + +
50R MET* 6.4 0.2 - - + -
180R TYR* 5.0 0.4 - - - +
238R ALA* 5.5 0.7 - - + -
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Residues in contact with ALA 202 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180O TYR* 4.0 18.8 - - + +
184O GLN* 3.7 35.0 + - + +
185O ASN 3.1 16.7 + - - +
186O THR* 3.9 2.9 + - - -
200O ARG 3.0 7.2 + - - -
201O ALA* 1.3 73.0 - - - +
203O ALA* 1.3 60.2 + - + +
204O GLU 3.3 1.5 + - - -
205O ASN 4.0 12.8 - - - +
207O ILE* 4.4 2.1 - - - +
234O ARG 5.4 0.3 - - - +
235O VAL 4.6 0.7 - - - -
236O PRO* 4.0 5.0 - - - +
186R THR* 3.9 19.1 - - + -
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Residues in contact with ALA 203 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180O TYR* 4.1 19.3 - - + -
186O THR 5.1 0.6 + - - +
201O ALA* 3.3 1.0 - - - +
202O ALA* 1.3 78.3 - - + +
204O GLU* 1.3 69.5 + - - +
236O PRO* 3.2 26.7 - - + +
236P PRO 4.6 1.9 - - - +
180R TYR* 4.2 8.9 + - - +
203R ALA* 3.6 31.6 - - + -
204R GLU* 4.9 1.6 - - - +
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Residues in contact with GLU 204 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201O ALA* 3.4 11.7 + - + +
202O ALA 3.3 0.6 - - - -
203O ALA* 1.3 90.6 - - - +
205O ASN* 1.3 68.8 + - - +
236O PRO* 4.2 0.9 - - - -
237P VAL* 3.8 14.0 - - - +
280P SER* 4.2 0.7 + - - -
281P SER* 4.1 7.1 - - - -
204Q GLU* 3.6 20.4 - - - +
49R THR* 3.9 17.9 - - + +
50R MET* 4.8 6.9 - - - +
180R TYR* 3.0 33.4 + - - +
203R ALA* 5.0 1.7 - - - +
236R PRO 4.7 6.1 - - - +
237R VAL* 5.7 0.7 - - - -
238R ALA* 3.8 25.8 + - + +
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Residues in contact with ASN 205 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200O ARG* 4.1 1.0 - - - +
201O ALA 2.9 23.0 + - - +
202O ALA 4.0 3.8 + - - +
204O GLU* 1.3 76.5 + - - +
206O ILE* 1.3 58.7 + - - +
207O ILE* 3.5 23.4 + - + +
234O ARG 3.4 8.8 - - - +
235O VAL* 3.9 0.5 - - - -
236O PRO* 3.4 19.0 - - - +
237P VAL* 3.8 7.2 - - - -
279P VAL* 3.3 17.2 - - + +
280P SER* 3.3 3.8 - - - +
281P SER* 2.6 51.5 + - - +
49R THR* 3.2 20.4 + - - +
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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
------------------------------------------------------------
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