Contacts of the helix formed by residues 261 - 270 (chain C) in PDB entry 3AP3
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 SER 261 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91C HIS* 3.5 33.8 + - - -
92C PRO* 3.9 12.1 - - - +
253C LEU* 4.4 1.0 - - - +
259C ALA 3.6 1.0 + - - -
260C TRP* 1.3 97.3 + - - +
262C ASP* 1.3 65.0 + - - +
263C ALA* 3.3 20.9 + - - +
264C VAL* 3.7 10.9 + - - +
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Residues in contact with ASP 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246C ARG* 3.8 22.7 + - - -
260C TRP* 3.2 14.5 + - + +
261C SER* 1.3 72.3 + - - +
263C ALA* 1.3 63.2 + - - +
264C VAL 3.2 2.6 + - - -
265C LEU* 3.5 11.0 + - - +
266C HIS* 3.2 33.3 + - - -
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Residues in contact with ALA 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C ALA* 3.8 19.6 - - - +
91C HIS 4.8 0.2 - - - +
92C PRO* 4.7 4.9 - - + -
261C SER* 3.2 16.0 + - - +
262C ASP* 1.3 77.9 - - - +
264C VAL* 1.3 56.4 + - - +
265C LEU 3.3 0.2 - - - -
266C HIS* 3.0 34.7 + - - +
267C HIS 3.7 1.7 + - - -
270C LEU* 4.2 20.3 - - + +
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Residues in contact with VAL 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C MET* 3.4 48.5 - - - +
88C LEU* 5.1 1.8 - - + +
90C ALA* 4.7 1.1 - - - +
91C HIS* 4.7 14.9 - - + +
249C LEU* 3.1 44.4 - - + -
253C LEU* 4.4 16.4 - - + -
260C TRP* 3.6 19.7 - - + -
261C SER* 3.7 13.2 + - - +
262C ASP 3.2 0.4 - - - -
263C ALA* 1.3 76.9 - - - +
265C LEU* 1.3 65.7 + - + +
266C HIS 3.2 1.3 + - - -
267C HIS* 4.2 3.3 + - - -
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Residues in contact with LEU 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C MET* 5.3 3.1 - - - -
245C PRO* 3.3 47.3 - - + +
246C ARG* 3.8 32.1 - - + +
249C LEU* 4.9 1.8 - - + -
260C TRP* 3.8 21.5 - - + -
262C ASP* 3.5 10.5 + - - +
263C ALA 3.3 1.0 - - - -
264C VAL* 1.3 90.0 - - + +
266C HIS* 1.3 68.5 + - + +
267C HIS* 3.7 5.2 - - - -
268C GLU* 3.9 7.9 - - - +
292C PRO* 5.8 0.9 - - - +
293C VAL* 5.4 5.0 - - + +
340C PHE* 3.2 36.4 - - + -
344C ASN* 5.3 0.3 + - - -
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Residues in contact with HIS 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C ASP* 3.2 44.8 + - - -
263C ALA* 3.0 13.0 + - - +
265C LEU* 1.3 92.1 + - + +
267C HIS* 1.3 54.1 + - - +
268C GLU* 3.1 17.6 + - - -
269C ASP* 2.7 46.8 + - + +
270C LEU* 3.9 5.4 + - + +
340C PHE* 4.6 14.7 - + - -
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Residues in contact with HIS 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C A3P 4.4 2.5 - - - -
83C LEU* 4.2 11.9 - - + +
86C ALA* 3.9 28.4 - - + +
87C MET* 3.7 30.5 - - + -
90C ALA* 4.1 14.4 - - + -
263C ALA 3.7 1.6 + - - -
264C VAL 4.2 3.6 + - - +
265C LEU 4.9 1.1 - - - -
266C HIS* 1.3 78.2 - - - +
268C GLU* 1.3 81.0 + - - +
269C ASP 2.9 1.4 + - - -
270C LEU* 3.0 16.7 + - - +
271C ILE* 3.8 12.0 + - - +
277C VAL* 4.0 4.7 - - + +
289C VAL* 3.1 30.0 + - + +
291C LYS 3.3 16.5 + - - -
293C VAL* 3.7 26.5 + - + +
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Residues in contact with GLU 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265C LEU 3.9 5.6 - - - +
266C HIS* 3.1 32.6 + - - -
267C HIS* 1.3 92.0 + - + +
269C ASP* 1.3 76.9 + - - +
270C LEU 3.3 1.1 + - - -
271C ILE* 3.7 17.1 + - - +
290C ILE 3.4 23.9 - - - +
291C LYS 4.1 1.6 - - - -
292C PRO* 3.8 34.2 - - + +
340C PHE* 5.9 0.7 - - - -
347C ARG* 4.0 13.8 + - - +
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Residues in contact with ASP 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266C HIS* 2.7 28.6 + - + +
268C GLU* 1.3 102.3 - - - +
270C LEU* 1.3 64.3 + - + +
271C ILE 3.8 1.1 - - - -
273C LYS* 3.1 24.8 + - - +
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Residues in contact with LEU 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C ALA* 3.5 38.1 - - + +
263C ALA* 4.2 17.5 - - + +
266C HIS* 4.4 6.1 - - + +
267C HIS 3.0 10.8 + - - +
269C ASP* 1.3 88.2 - - + +
271C ILE* 1.3 63.0 + - - +
273C LYS* 3.4 32.6 + - + +
274C PRO 5.5 2.9 - - - +
276C GLY* 4.3 11.7 - - - -
277C VAL* 3.0 24.7 + - + +
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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