Contacts of the helix formed by residues 249 - 260 (chain A) in PDB entry 3PEY
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 GLY 249 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247A GLN 3.4 1.0 + - - -
248A GLN* 1.3 82.1 + - - +
250A LEU* 1.3 64.6 + - - -
251A GLY 3.2 1.4 + - - +
252A ASP* 3.3 14.3 + - - +
253A GLN* 3.0 36.6 + - - +
4B U 3.3 15.5 - - - -
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Residues in contact with LEU 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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170A PRO* 3.8 27.1 - - + -
216A PRO* 3.7 22.9 - - + -
243A ASN* 3.8 15.7 - - - +
244A MET* 3.3 22.4 - - - +
247A GLN* 3.9 11.0 - - + -
248A GLN 2.9 7.3 + - - -
249A GLY* 1.3 70.4 - - - -
251A GLY* 1.3 59.1 + - - +
253A GLN* 3.7 5.0 - - - +
254A CYS* 2.8 35.2 + - - -
3B U 3.3 27.4 - - - +
4B U 3.4 34.5 + - - +
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Residues in contact with GLY 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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244A MET 3.1 15.7 + - - -
245A LEU* 3.5 20.3 - - - +
247A GLN 2.9 17.1 + - - -
250A LEU* 1.3 77.0 - - - +
252A ASP* 1.3 64.2 + - - +
254A CYS* 4.0 2.1 - - - +
255A ILE* 3.3 26.0 + - - +
281A TYR* 5.7 1.1 - - - -
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Residues in contact with ASP 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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247A GLN 4.8 0.2 + - - -
249A GLY* 3.3 14.0 + - - +
251A GLY* 1.3 76.7 - - - +
253A GLN* 1.3 65.7 + - + +
255A ILE* 3.3 7.7 + - - +
256A ARG* 2.9 51.7 + - - +
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Residues in contact with GLN 253 (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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216A PRO* 3.6 14.8 - - + +
217A GLY* 3.5 10.0 + - - -
220A LEU* 4.1 25.1 - - + +
249A GLY* 3.0 26.1 + - - +
250A LEU* 3.8 2.9 - - - +
252A ASP* 1.3 79.7 - - + +
254A CYS* 1.3 57.5 + - - +
256A ARG* 3.3 3.8 + - - +
257A VAL* 2.9 34.5 + - - +
4B U 2.5 38.0 + - - +
5B U 5.4 2.2 - - - -
1009B NO3 3.0 25.8 + - - -
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Residues in contact with CYS 254 (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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168A LEU* 4.2 3.8 - - - -
216A PRO* 3.9 11.9 - - - -
236A PHE* 4.2 4.0 - - - -
238A LEU* 3.9 28.7 - - + -
244A MET* 3.8 42.8 - - - +
245A LEU* 5.0 5.4 - - + -
250A LEU 2.8 24.6 + - - +
251A GLY 4.0 3.4 - - - +
253A GLN* 1.3 77.8 - - - +
255A ILE* 1.3 58.8 + - - +
257A VAL* 3.4 7.7 + - - +
258A LYS* 2.9 28.9 + - - +
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Residues in contact with ILE 255 (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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245A LEU* 4.5 7.6 - - + -
251A GLY 3.3 14.5 + - - +
252A ASP* 3.3 10.5 + - - +
253A GLN 3.2 0.2 - - - -
254A CYS* 1.3 78.4 - - - +
256A ARG* 1.3 62.5 + - + +
258A LYS* 3.3 6.8 + - + +
259A ARG* 3.1 40.9 + - - +
281A TYR* 3.9 15.9 - - - +
285A ILE* 3.7 44.6 - - + -
1005A NO3 3.5 21.1 - - - +
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Residues in contact with ARG 256 (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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220A LEU* 3.9 16.4 - - + -
224A ARG* 3.7 18.0 - - - +
252A ASP* 2.9 57.6 + - - +
253A GLN* 3.8 5.6 - - - +
255A ILE* 1.3 79.3 - - + +
257A VAL* 1.3 61.8 + - - +
259A ARG* 3.3 16.4 + - - +
260A PHE* 3.2 19.8 + - - -
1007A NO3 3.3 25.2 + - - +
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Residues in contact with VAL 257 (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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166A ILE* 5.4 0.4 - - + -
168A LEU* 4.2 13.7 - - + -
216A PRO 4.2 5.6 - - - +
219A VAL* 4.3 6.1 - - + -
220A LEU* 3.8 34.3 - - + +
223A MET* 3.7 28.3 - - + -
236A PHE* 3.7 26.9 - - + -
253A GLN 2.9 22.0 + - - +
254A CYS 3.7 4.9 - - - +
256A ARG* 1.3 75.1 - - - +
258A LYS* 1.3 64.3 + - - +
260A PHE* 3.0 20.5 + - - +
261A LEU* 3.6 7.0 - - + +
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Residues in contact with LYS 258 (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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236A PHE* 3.9 21.7 - - + -
254A CYS 2.9 18.3 + - - +
255A ILE* 3.5 7.0 - - + +
257A VAL* 1.3 75.5 - - - +
259A ARG* 1.3 59.6 + - - +
261A LEU* 3.0 32.5 + - + +
267A LEU* 3.6 29.9 - - + +
285A ILE* 3.3 38.5 + - + -
286A VAL* 5.8 0.7 - - + -
1005A NO3 3.1 32.1 + - - +
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Residues in contact with ARG 259 (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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255A ILE* 3.1 28.6 + - - +
256A ARG* 3.8 11.0 - - - +
257A VAL 3.1 1.0 - - - -
258A LYS* 1.3 76.5 - - - +
260A PHE* 1.3 59.8 + - + +
261A LEU 3.3 4.4 - - - +
1005A NO3 3.0 42.0 + - - +
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Residues in contact with PHE 260 (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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220A LEU* 3.8 22.2 - - + -
223A MET* 3.7 37.7 - - + -
224A ARG* 4.1 22.9 - - + -
230A LEU* 3.6 30.7 - - + +
231A GLN* 5.0 4.2 - - - +
256A ARG 3.2 21.3 - - - -
257A VAL* 3.0 9.1 + - - +
259A ARG* 1.3 77.5 - - - +
261A LEU* 1.3 62.7 + - + +
262A PRO* 4.1 0.3 - - - +
1007A NO3 3.9 22.9 - - - -
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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