Contacts of the helix formed by residues 339 - 352 (chain B) in PDB entry 2P5G
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 GLN 339 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335B ASP* 2.9 28.0 + - - +
336B ALA* 3.3 28.6 + - - +
337B LYS 4.0 4.3 - - - +
338B ARG* 1.3 81.2 - - - +
340B PHE* 1.3 61.5 + - - +
341B ILE 3.7 1.1 - - - -
342B ASN* 3.9 23.1 + - + +
343B LEU* 3.5 20.0 + - - +
554B THR* 5.6 4.3 + - - +
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Residues in contact with PHE 340 (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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273B TYR* 3.3 32.1 + + - +
276B LEU* 3.6 17.9 - - + -
277B TYR* 3.4 44.4 - + - -
280B PHE* 3.3 41.3 - - + -
281B SER* 3.5 13.5 - - - -
297B GLU* 5.7 0.2 - - - -
335B ASP* 3.5 0.2 + - - -
338B ARG* 3.7 28.5 - - + -
339B GLN* 1.3 73.9 - - - +
341B ILE* 1.3 62.8 + - - +
342B ASN 3.2 1.8 - - - -
343B LEU* 2.9 18.9 + - + +
344B SER* 2.8 30.7 + - - -
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Residues in contact with ILE 341 (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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110B VAL* 3.9 33.0 - - + -
112B ASN* 4.8 2.7 - - - +
212B ILE* 4.5 13.5 - - + -
214B THR* 3.5 34.3 - - + +
271B LEU* 4.7 3.3 - - + +
273B TYR* 3.7 11.0 - - + -
276B LEU* 3.7 21.1 - - + -
332B LEU* 6.2 0.4 - - + -
335B ASP* 3.2 27.4 + - - +
340B PHE* 1.3 76.6 - - - +
342B ASN* 1.3 62.2 + - - +
344B SER* 3.3 8.4 + - - -
345B LEU* 3.2 30.6 + - + +
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Residues in contact with ASN 342 (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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103B TYR* 2.9 31.5 + - - -
105B HIS* 4.3 16.3 - - + +
335B ASP* 4.7 0.6 + - - -
339B GLN* 3.9 27.3 + - + +
340B PHE 3.2 0.4 - - - -
341B ILE* 1.3 76.7 - - - +
343B LEU* 1.3 60.2 + - - +
345B LEU* 3.3 8.3 + - + +
346B ASP* 3.0 25.6 + - - +
554B THR* 4.0 21.6 + - - +
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Residues in contact with LEU 343 (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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280B PHE* 3.3 31.0 - - + +
338B ARG 5.8 0.2 - - - +
339B GLN 3.5 13.8 + - - +
340B PHE* 2.9 28.7 + - + +
342B ASN* 1.3 78.5 - - - +
344B SER* 1.3 54.9 + - - +
346B ASP 3.4 0.3 + - - -
347B MSE 3.0 12.8 + - - +
554B THR* 3.6 29.2 - - + +
557B ILE* 3.6 29.2 - - + -
558B ASN* 3.0 53.5 + - - +
561B LEU* 4.0 2.2 - - + -
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Residues in contact with SER 344 (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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271B LEU* 3.1 36.3 - - - +
276B LEU* 3.3 19.1 - - - +
280B PHE* 4.2 7.9 - - - -
340B PHE 2.8 11.3 + - - -
341B ILE 3.4 5.2 - - - -
342B ASN 3.3 0.2 - - - -
343B LEU* 1.3 72.7 - - - +
345B LEU* 1.3 54.7 + - - +
347B MSE 3.2 7.2 + - - +
348B GLY* 2.7 32.9 + - - -
355B ILE* 4.3 3.7 - - - +
358B VAL* 3.6 18.6 - - - +
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Residues in contact with LEU 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B TYR* 3.7 17.3 - - + -
105B HIS* 4.7 7.0 - - + -
108B ILE* 3.7 27.8 - - + -
110B VAL* 5.2 2.9 - - + -
212B ILE* 3.7 29.6 - - + -
341B ILE* 3.2 27.0 + - + +
342B ASN* 3.3 16.1 + - - +
344B SER* 1.3 79.3 - - - +
346B ASP* 1.3 58.2 + - - +
347B MSE 3.2 0.2 + - - -
348B GLY* 3.2 1.2 + - - -
349B TYR* 2.8 58.3 + - + +
355B ILE* 4.1 11.9 - - + -
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Residues in contact with ASP 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B TYR* 3.4 23.9 + - - +
342B ASN 3.0 16.3 + - - +
345B LEU* 1.3 75.1 - - - +
347B MSE 1.3 60.4 + - - +
349B TYR* 4.1 1.4 - - - +
350B TYR* 3.1 25.6 + - - +
551B ALA 5.4 1.6 - - - +
554B THR* 3.7 21.7 - - + +
555B ALA* 4.0 7.7 - - - +
558B ASN* 2.8 27.5 + - - +
559B ARG* 3.9 16.0 + - - -
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Residues in contact with MSE 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B PHE* 5.4 5.2 - - + -
343B LEU 3.0 13.9 + - - +
344B SER* 3.3 10.1 - - - +
346B ASP* 1.3 74.4 - - - +
348B GLY* 1.3 66.6 + - - +
350B TYR* 2.9 18.9 + - - +
351B ALA* 3.0 14.2 + - - +
353B ILE* 5.3 0.2 - - + -
358B VAL* 3.5 26.5 - - + +
364B THR* 4.2 14.4 - - + -
558B ASN* 3.2 51.3 - - - +
561B LEU* 3.9 18.6 - - + -
562B LEU* 3.8 36.8 - - + +
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Residues in contact with GLY 348 (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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5B TYR* 2.9 13.8 + - - -
344B SER 2.7 19.4 + - - -
345B LEU 3.7 0.9 - - - -
347B MSE 1.3 72.8 - - - +
349B TYR* 1.3 57.0 + - - +
352B LYS 2.8 24.4 + - - -
353B ILE* 3.1 21.3 + - - -
355B ILE* 4.0 13.2 - - - -
358B VAL* 3.7 6.7 - - - +
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Residues in contact with TYR 349 (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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4B PHE* 3.7 16.3 - + + -
5B TYR* 2.9 59.0 + + - -
6B LEU* 4.0 9.5 + - - +
101B ILE* 3.5 53.4 + - + +
103B TYR* 3.8 29.2 - + + -
108B ILE* 3.8 10.4 - - - +
211B VAL* 5.8 0.3 - - - +
345B LEU* 2.8 57.2 + - + +
346B ASP 4.5 2.2 - - - +
348B GLY* 1.3 71.4 - - - +
350B TYR* 1.3 64.7 + - - +
352B LYS* 3.7 6.2 - - - +
355B ILE* 3.9 9.8 - - + +
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Residues in contact with TYR 350 (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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346B ASP* 3.1 21.7 + - - +
347B MSE 2.9 9.5 + - - +
349B TYR* 1.3 81.2 - - - +
351B ALA* 1.3 65.8 + - + +
352B LYS* 4.3 6.6 + - - +
368B ILE* 3.6 31.6 - - + +
371B ASN* 6.0 0.5 - - - +
477B LYS* 5.7 1.4 - - - -
478B VAL* 3.8 16.1 - - - +
481B GLN* 2.6 39.1 + - - -
559B ARG* 3.4 30.7 - - - +
562B LEU* 3.7 18.8 - - + -
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Residues in contact with ALA 351 (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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347B MSE 3.0 12.5 + - - +
350B TYR* 1.3 77.6 - - + +
352B LYS* 1.3 59.3 + - - +
353B ILE* 4.1 16.6 - - + -
364B THR* 3.9 22.0 - - + +
367B ALA* 3.7 9.0 - - + +
368B ILE* 3.8 27.9 - - + +
371B ASN* 2.8 31.2 + - - +
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Residues in contact with LYS 352 (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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5B TYR* 3.6 8.7 - - + -
90B LEU* 4.1 11.6 - - - +
93B LEU* 3.4 34.9 - - + +
94B SER* 4.5 2.4 + - - +
97B TYR 3.1 28.8 + - - +
98B ASN* 4.7 2.2 - - - +
99B TYR 3.2 23.8 + - - +
100B GLU* 5.0 1.4 - - - +
101B ILE* 3.8 17.7 - - + +
348B GLY 2.8 12.4 + - - -
349B TYR 3.7 12.6 - - - +
350B TYR 3.4 4.8 + - - +
351B ALA* 1.3 81.8 - - - +
353B ILE* 1.3 62.6 + - - +
367B ALA* 4.5 0.9 - - - +
371B ASN* 3.8 27.9 + - - +
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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