Contacts of the helix formed by residues 244 - 257 (chain B) in PDB entry 3AP2
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 244 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240B GLN* 2.9 24.8 + - + +
241B LEU 3.5 2.5 - - - -
243B LEU* 1.3 86.6 + - + +
245B PRO* 1.3 62.9 - - - +
246B ARG 3.4 2.2 - - - -
247B ARG* 3.0 56.0 + - + +
248B SER* 2.7 30.1 + - - +
335B GLY* 5.3 1.2 - - - -
336B ASN* 3.0 34.8 + - + -
338B ASP* 2.6 32.4 + - - +
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Residues in contact with PRO 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B MET* 5.7 0.2 - - - -
241B LEU* 3.2 16.6 - - + +
242B VAL 3.3 10.5 - - - +
243B LEU 3.6 2.9 - - - +
244B HIS* 1.3 85.0 - - - +
246B ARG* 1.3 53.9 + - - +
248B SER* 3.2 2.5 + - - -
249B LEU* 2.7 46.6 + - + +
265B LEU* 3.9 18.4 - - + -
293B VAL* 3.9 15.5 - - + -
338B ASP* 4.2 5.2 - - - +
340B PHE* 3.8 18.6 - - + -
341B VAL* 3.3 27.4 - - + -
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Residues in contact with ARG 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B HIS 3.4 0.4 - - - -
245B PRO* 1.3 76.6 - - + +
247B ARG* 1.3 69.2 + - - +
250B LYS* 3.0 52.3 + - + +
260B TRP* 3.9 14.1 - - + +
262B ASP* 3.3 23.6 + - - -
265B LEU* 3.6 36.0 - - + +
266B HIS* 6.1 1.8 - - - -
338B ASP* 4.9 5.5 + - - +
340B PHE* 5.9 8.5 - - + -
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Residues in contact with ARG 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B GLN* 4.2 10.5 - - - +
244B HIS* 3.0 63.9 + - + +
245B PRO 3.4 0.4 - - - -
246B ARG* 1.3 82.1 - - + +
248B SER* 1.3 62.9 + - - +
250B LYS* 3.3 7.8 + - - +
251B LEU* 3.3 35.7 + - + +
338B ASP* 5.0 2.5 + - - +
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Residues in contact with SER 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B VAL* 5.7 2.0 - - - -
240B GLN* 3.0 22.3 + - - +
241B LEU* 3.4 24.8 + - - -
244B HIS* 2.7 23.7 + - - +
245B PRO 3.5 2.9 - - - -
247B ARG* 1.3 75.4 + - - +
249B LEU* 1.3 63.5 + - - +
251B LEU* 3.1 13.0 + - - +
252B ILE* 3.1 30.8 + - - +
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Residues in contact with LEU 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B MET* 4.0 21.5 - - + -
87B MET* 3.8 21.8 - - + -
88B LEU* 4.7 6.5 - - + -
241B LEU* 3.4 32.5 - - + -
245B PRO* 2.7 24.3 + - + +
248B SER* 1.3 73.2 - - - +
250B LYS* 1.3 61.7 + - - +
252B ILE* 4.3 5.6 - - + -
253B LEU* 3.0 37.5 + - + +
260B TRP* 3.8 18.8 - - + -
264B VAL* 3.6 32.8 - - + -
265B LEU* 4.6 3.8 - - + -
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Residues in contact with LYS 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B ARG* 3.0 43.5 + - + +
247B ARG* 3.4 8.5 - - - +
249B LEU* 1.3 77.2 - - - +
251B LEU* 1.3 62.7 + - + +
253B LEU* 4.2 1.7 - - - +
254B ASP* 3.1 34.2 + - - +
260B TRP* 3.3 51.2 - - + +
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Residues in contact with LEU 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B LEU* 4.6 6.9 - - + +
247B ARG* 3.3 30.2 + - + +
248B SER* 3.1 11.3 + - - +
250B LYS* 1.3 76.8 - - + +
252B ILE* 1.3 60.4 + - + +
254B ASP* 3.3 6.8 - - + +
255B PHE* 2.9 30.0 + - - +
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Residues in contact with ILE 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B MET* 3.8 34.3 - - + -
88B LEU* 4.4 4.0 - - + -
179B LEU* 3.8 30.7 - - + -
234B LEU* 4.0 21.5 - - + -
236B VAL* 3.8 21.8 - - + -
241B LEU* 4.5 6.5 - - + -
248B SER* 3.1 23.6 + - - +
249B LEU* 3.9 9.6 - - + +
250B LYS 3.4 0.2 - - - -
251B LEU* 1.3 73.2 - - + +
253B LEU* 1.3 54.8 + - - +
255B PHE* 3.2 5.0 + - - +
256B LEU* 2.8 47.3 + - + +
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Residues in contact with LEU 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B LEU* 4.3 24.0 - - + -
91B HIS* 4.3 19.1 - - + -
94B VAL* 6.1 1.8 - - + -
249B LEU* 3.0 26.2 + - + +
250B LYS* 4.2 2.7 - - - +
252B ILE* 1.3 75.3 - - - +
254B ASP* 1.3 62.2 + - - +
256B LEU* 3.1 11.4 + - + -
257B GLY 3.0 4.0 + - - -
258B ILE* 2.9 44.4 + - + +
259B ALA 3.6 20.6 - - - +
260B TRP* 3.9 29.6 - - + +
261B SER 4.3 1.6 - - - +
264B VAL* 4.6 10.3 - - + -
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Residues in contact with ASP 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250B LYS* 3.1 23.0 + - - +
251B LEU* 3.3 12.3 - - + +
253B LEU* 1.3 75.6 - - - +
255B PHE* 1.3 54.8 + - - +
257B GLY* 2.7 28.2 + - - -
258B ILE 4.0 2.9 + - - -
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Residues in contact with PHE 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B LYS* 3.6 26.7 - - + +
178B PHE 4.0 9.0 - - - -
179B LEU* 4.3 2.5 - - + -
230B LYS 3.4 25.4 - - - -
231B GLU* 3.4 17.3 - - - +
232B LYS* 3.4 26.9 - - - -
233B CYS 4.1 1.6 - - - -
234B LEU* 3.6 45.3 - - + -
251B LEU 2.9 16.6 + - - +
252B ILE 3.3 8.1 - - - +
254B ASP* 1.3 70.8 - - - +
256B LEU* 1.3 85.1 + - + +
257B GLY 3.4 0.5 + - - -
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Residues in contact with LEU 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ILE* 3.8 36.3 - - + -
88B LEU* 3.9 26.9 - - + -
94B VAL* 5.9 0.2 - - + -
177B LYS* 4.2 22.6 - - + +
179B LEU* 4.1 13.7 - - + -
252B ILE* 2.8 30.6 + - + +
253B LEU* 3.1 12.3 + - + +
254B ASP 3.1 0.2 + - - -
255B PHE* 1.3 96.2 - - + +
257B GLY* 1.3 60.8 + - - +
258B ILE* 3.4 25.2 + - + +
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Residues in contact with GLY 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B ARG* 5.2 3.6 + - - -
177B LYS* 5.8 0.7 - - - -
254B ASP 2.7 23.0 + - - -
255B PHE 3.2 2.2 + - - -
256B LEU* 1.3 71.9 - - - +
258B ILE* 1.3 60.1 + - - +
259B ALA 4.4 0.2 + - - -
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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