Contacts of the helix formed by residues 249 - 258 (chain A) in PDB entry 1PVS
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 THR 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 GLY 4.5 4.9 - - - +
248A MET* 1.3 73.8 - - - +
250A PRO* 1.3 78.0 - - - +
251A ALA* 3.6 7.9 + - - +
252A GLN* 2.9 37.7 + - - +
253A ILE* 2.9 24.4 + - - +
34B TYR* 3.7 32.1 - - + +
49B THR* 5.5 0.9 - - - +
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Residues in contact with PRO 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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236A PRO* 3.3 28.4 - - + +
237A ASP* 3.9 18.8 - - - +
242A LYS* 3.6 26.9 - - - +
248A MET 4.7 0.7 - - - +
249A THR* 1.3 88.7 - - - +
251A ALA* 1.3 56.4 + - - +
253A ILE* 3.3 2.2 + - + -
254A ARG* 2.9 36.1 + - - +
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Residues in contact with ALA 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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249A THR* 3.2 8.6 + - - +
250A PRO* 1.3 79.6 - - - +
252A GLN* 1.3 57.5 + - - +
254A ARG* 3.4 15.8 + - - +
255A ARG* 3.0 26.2 + - - +
1B MET* 3.7 5.7 - - - +
49B THR* 4.1 26.9 - - + +
51B ILE* 3.9 4.0 - - + +
62B ASN* 4.0 23.8 - - + +
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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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247A GLY 4.0 2.6 - - - +
248A MET* 3.2 26.8 - - + +
249A THR* 2.9 43.5 + - - +
251A ALA* 1.3 74.8 - - + +
253A ILE* 1.3 61.5 + - - +
255A ARG* 3.2 4.8 + - - +
256A TYR* 2.8 28.1 + - - +
33B SER* 2.8 32.1 + - - -
34B TYR* 3.3 26.7 - - + +
49B THR* 5.8 0.2 - - + -
51B ILE* 4.1 23.5 - - + +
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Residues in contact with ILE 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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234A PHE* 3.9 14.4 - - + -
236A PRO* 3.9 23.1 - - + +
241A ILE* 3.9 25.6 - - + -
242A LYS* 4.4 11.2 - - + +
245A PHE* 3.6 43.1 - - + +
248A MET* 3.6 21.3 - - + +
249A THR 2.9 12.9 + - - +
250A PRO 3.6 5.2 - - - +
252A GLN* 1.3 76.1 - - - +
254A ARG* 1.3 57.4 + - - +
256A TYR* 3.1 7.2 + - - +
257A ALA* 2.9 29.0 + - - +
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Residues in contact with ARG 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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217A ARG* 5.3 12.5 - - - +
234A PHE* 5.5 3.6 - - + -
236A PRO* 3.9 31.5 - - + +
237A ASP* 5.0 5.5 + - - -
250A PRO* 2.9 25.1 + - - +
251A ALA* 3.5 19.9 - - - +
253A ILE* 1.3 77.8 - - - +
255A ARG* 1.3 60.2 + - - +
257A ALA* 3.6 10.4 + - - +
258A GLU* 3.3 19.6 + - + +
264A ARG* 5.0 6.7 + - - +
1B MET* 3.9 9.9 - - + +
62B ASN* 2.8 47.3 + - - +
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Residues in contact with ARG 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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251A ALA 3.0 14.1 + - - +
252A GLN* 3.4 9.4 - - - +
253A ILE 3.2 0.2 - - - -
254A ARG* 1.3 76.0 - - - +
256A TYR* 1.3 67.8 + - - +
257A ALA 3.4 0.2 + - - -
258A GLU* 3.0 40.8 + - - +
259A ARG* 5.3 3.6 - - - +
1B MET* 3.9 13.2 - - + +
51B ILE* 4.2 22.9 - - + -
53B ASP* 3.4 17.8 + - - +
56B ARG* 4.8 8.3 - - - +
60B HIS* 3.3 49.3 + - + -
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Residues in contact with TYR 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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245A PHE* 3.8 14.8 - + + -
248A MET* 5.0 9.0 - - - -
252A GLN 2.8 13.2 + - - +
253A ILE* 3.1 11.6 + - - +
255A ARG* 1.3 81.0 - - - +
257A ALA* 1.3 57.5 + - - +
258A GLU 3.3 0.9 + - - -
259A ARG* 3.0 74.7 + - - +
260A TRP* 3.5 32.3 - + - -
277A TRP* 3.9 9.9 - + - -
279A PRO* 3.5 22.6 - - + +
280A ASP* 2.8 35.9 + - + +
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Residues in contact with ALA 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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234A PHE* 3.7 35.7 - - + -
245A PHE* 6.2 0.2 - - + -
253A ILE 2.9 15.9 + - - +
254A ARG* 4.1 5.6 - - - +
255A ARG 3.3 0.4 - - - -
256A TYR* 1.3 72.9 - - - +
258A GLU* 1.3 61.0 + - - +
259A ARG 3.0 5.6 - - - -
260A TRP* 3.0 36.7 + - + -
264A ARG* 3.4 20.3 - - - +
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Residues in contact with GLU 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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254A ARG* 3.3 18.8 - - + +
255A ARG* 3.0 37.8 + - - +
256A TYR 3.3 1.2 - - - -
257A ALA* 1.3 76.6 - - - +
259A ARG* 1.3 60.2 + - - +
260A TRP 3.1 1.9 + - - -
261A LYS* 3.2 21.0 + - + +
264A ARG* 4.2 21.3 + - - +
1B MET* 3.0 40.1 - - - +
60B HIS* 4.2 4.5 + - - -
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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