Contacts of the helix formed by residues 240 - 253 (chain A) in PDB entry 2PPQ
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 ASN 240 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A ALA* 5.9 0.2 - - - +
232A CYS 2.8 21.2 + - - +
234A GLU* 2.9 36.2 + - + +
238A ALA 3.5 0.6 + - - -
239A TYR* 1.3 76.1 - - - +
241A VAL* 1.3 57.3 + - - +
242A THR* 2.9 24.7 + - - -
243A LYS* 3.1 30.3 + - + +
244A GLY 3.0 22.5 + - - -
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Residues in contact with VAL 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A TYR* 3.6 29.8 + - + +
240A ASN* 1.3 72.7 + - - +
242A THR* 1.3 57.4 + - - +
245A LYS* 2.9 30.7 + - + +
315A ALA 5.2 0.4 - - - +
316A GLU 4.1 9.2 - - - +
317A TYR 3.8 1.6 - - - +
318A GLY* 3.4 26.9 - - - +
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Residues in contact with THR 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ALA* 3.6 18.3 - - + +
240A ASN* 2.9 13.5 + - - -
241A VAL* 1.3 79.3 - - - +
243A LYS* 1.3 58.6 + - - +
245A LYS* 3.8 8.6 + - + +
246A ALA* 3.2 22.9 + - - +
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Residues in contact with LYS 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A PRO* 3.3 32.9 + - - +
114A GLU* 4.3 2.0 - - - +
115A ALA* 3.8 29.6 - - + +
118A CYS* 3.8 15.0 - - - +
231A TRP 3.4 19.8 + - - +
232A CYS* 3.6 12.0 - - - -
233A PHE 5.1 3.4 + - - -
234A GLU* 3.1 27.5 + - - +
240A ASN* 3.1 32.1 + - + +
242A THR* 1.3 73.9 - - - +
244A GLY* 1.3 61.6 + - - +
246A ALA* 3.3 2.7 + - - +
247A LEU* 2.9 30.3 + - - +
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Residues in contact with GLY 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A LEU* 4.2 3.4 - - - -
232A CYS* 3.6 13.6 - - - -
239A TYR* 3.3 24.2 - - - -
240A ASN 3.0 10.9 + - - -
241A VAL 3.4 0.2 + - - -
242A THR 3.4 0.2 - - - -
243A LYS* 1.3 75.2 - - - +
245A LYS* 1.3 60.5 + - - +
247A LEU* 3.3 1.7 + - - +
248A LEU* 3.0 31.9 + - - +
317A TYR 3.5 6.3 - - - -
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Residues in contact with LYS 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ARG* 4.4 5.8 - - - +
241A VAL* 2.9 21.9 + - + +
242A THR* 3.8 8.5 - - + +
244A GLY* 1.3 71.5 - - - +
246A ALA* 1.3 56.8 + - - +
248A LEU* 3.9 1.1 - - - -
249A GLU* 2.9 71.2 + - + +
317A TYR 3.5 3.0 + - - -
318A GLY* 3.2 30.5 - - - +
319A LEU 4.6 0.7 - - - +
320A ALA 5.4 4.9 - - - -
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Residues in contact with ALA 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ALA* 3.1 33.0 - - + +
116A LYS* 5.2 0.2 - - - -
118A CYS* 4.1 0.2 - - + -
119A ARG* 3.3 37.4 - - + +
242A THR 3.2 16.0 + - - +
243A LYS 3.3 4.9 + - - +
245A LYS* 1.3 78.1 - - - +
247A LEU* 1.3 55.1 + - - +
249A GLU* 3.8 0.3 - - - +
250A GLY 2.8 29.1 + - - -
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Residues in contact with LEU 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A CYS* 3.5 25.3 + - + +
121A VAL* 4.0 15.9 - - + -
122A GLY* 3.5 25.4 - - - +
125A LEU* 6.0 2.0 - - + -
224A VAL* 4.2 8.5 - - + +
227A CYS* 3.8 17.9 - - + +
228A LEU* 3.7 44.6 - - + +
231A TRP* 5.2 3.4 - - + -
232A CYS* 4.1 6.7 - - - -
243A LYS 2.9 17.1 + - - +
244A GLY 3.6 2.9 - - - +
246A ALA* 1.3 77.7 - - - +
248A LEU* 1.3 65.2 + - + +
251A TYR* 2.9 26.0 + - + +
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Residues in contact with LEU 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A VAL* 3.5 31.6 - - + -
228A LEU* 4.3 15.9 - - + -
244A GLY 3.0 20.8 + - - +
245A LYS 4.2 1.6 - - - +
247A LEU* 1.3 78.1 - - + +
249A GLU* 1.3 59.6 + - - +
251A TYR* 3.3 5.6 + - + +
252A GLN* 2.8 35.9 + - + +
257A LEU* 4.7 7.8 - - + +
265A LEU* 4.1 21.3 - - + -
314A VAL* 4.3 3.8 - - + -
317A TYR* 3.9 27.6 - - + +
319A LEU* 4.1 32.8 - - + -
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Residues in contact with GLU 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A ARG* 2.9 35.5 + - - +
245A LYS* 2.9 57.5 + - + +
248A LEU* 1.3 68.1 - - - +
250A GLY* 1.3 66.2 + - - +
252A GLN* 3.3 7.5 + - - +
253A SER* 2.9 24.6 + - - -
318A GLY 5.0 0.7 - - - +
319A LEU* 3.7 21.0 - - + +
320A ALA 4.9 6.9 + - - +
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Residues in contact with GLY 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A ARG* 3.7 26.3 - - - +
123A LYS* 3.3 20.9 - - - +
246A ALA 2.8 22.9 + - - -
247A LEU 3.7 0.7 - - - -
249A GLU* 1.3 73.4 - - - +
251A TYR* 1.3 59.9 + - - +
253A SER* 2.6 26.1 + - - -
254A VAL 3.8 0.9 + - - -
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Residues in contact with TYR 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A GLY* 3.2 28.7 - - - +
125A LEU* 4.0 7.6 - - + -
126A ALA* 3.4 26.3 - - + +
129A HIS* 2.7 32.2 + + - -
220A LEU* 4.1 1.0 - - - +
224A VAL* 3.6 26.4 - - + +
247A LEU* 2.9 18.1 + - + +
248A LEU* 3.6 7.0 - - - +
249A GLU 3.3 0.2 - - - -
250A GLY* 1.3 74.3 - - - +
252A GLN* 1.3 60.1 + - - +
254A VAL 3.1 3.5 + - - -
255A ARG* 2.9 71.7 + - + -
257A LEU* 3.6 30.7 - - + -
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Residues in contact with GLN 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A LEU 2.8 32.0 + - - +
249A GLU* 3.3 7.4 + - - +
251A TYR* 1.3 72.6 - - - +
253A SER* 1.3 61.2 + - - +
254A VAL 3.0 2.1 + - - -
255A ARG 3.8 3.8 - - - -
256A PRO* 3.5 27.9 - - + +
257A LEU* 2.5 65.3 + - + +
262A LEU* 4.8 5.5 - - - +
319A LEU* 4.4 22.3 - - + +
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Residues in contact with SER 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ARG* 5.9 1.8 - - - -
123A LYS* 3.5 22.9 - - - +
249A GLU 2.9 14.5 + - - -
250A GLY* 2.6 22.0 + - - -
252A GLN* 1.3 76.4 - - - +
254A VAL* 1.3 60.8 + - - +
256A PRO* 5.5 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