Contacts of the helix formed by residues 347 - 360 (chain B) in PDB entry 3K5N
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 GLU 347 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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343B PHE 2.8 12.5 + - - -
344B HIS* 3.6 14.9 - - - +
345B LYS 3.2 4.5 - - - +
346B THR* 1.3 92.0 + - - +
348B ILE* 1.3 60.9 + - - +
349B MET 3.4 2.6 + - - -
350B PRO* 3.8 20.4 - - + +
351B PHE* 3.5 15.6 + - - +
487B PRO* 5.9 4.9 - - + +
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Residues in contact with ILE 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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275B ILE* 5.3 0.2 - - + -
277B GLY* 4.9 0.9 - - - +
280B ALA* 3.9 39.0 - - + +
281B LEU* 3.9 24.2 - - + +
284B ALA* 4.3 13.5 - - + -
286B TRP* 4.8 3.8 - - - +
342B ILE* 5.7 0.4 - - + -
343B PHE* 3.6 32.7 + - + +
346B THR* 3.2 14.5 - - - +
347B GLU* 1.3 70.8 - - - +
349B MET* 1.3 70.4 + - - +
350B PRO 3.0 2.2 - - - -
351B PHE* 2.6 20.1 + - + -
352B LEU* 2.5 31.4 + - + +
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Residues in contact with MET 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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150B LEU* 4.3 13.0 - - + -
152B TRP* 3.6 39.0 - - + +
219B VAL* 4.2 24.5 - - + -
273B LEU* 4.0 27.8 - - + -
275B ILE* 4.4 18.6 - - + -
343B PHE* 4.5 13.7 + - + -
347B GLU* 3.4 0.4 - - - +
348B ILE* 1.3 89.1 - - - +
350B PRO* 1.3 70.5 - - + +
352B LEU* 2.9 21.7 + - + +
353B LEU* 3.2 25.2 + - + +
363B VAL* 4.5 4.5 - - + -
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Residues in contact with PRO 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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152B TRP* 5.1 3.8 - - + -
343B PHE 5.5 0.9 - - - +
347B GLU* 3.8 26.2 - - + +
348B ILE 3.6 0.7 - - - -
349B MET* 1.3 100.9 - - + +
351B PHE* 1.3 59.2 + - - +
353B LEU* 3.5 11.9 + - + +
354B GLU* 3.2 25.5 + - - +
487B PRO* 4.7 11.4 - - + +
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Residues in contact with PHE 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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283B SER* 4.5 9.6 - - - -
284B ALA* 4.3 23.3 - - + -
347B GLU 3.5 10.4 + - - +
348B ILE* 2.6 21.1 + - + +
350B PRO* 1.3 75.7 - - - +
352B LEU* 1.3 99.0 + - + +
354B GLU* 3.8 3.0 - - - +
355B ARG* 3.3 39.7 + - - +
487B PRO* 4.2 30.2 - - + +
490B GLN* 4.3 24.7 - - + -
491B ALA* 4.7 9.4 - - - +
494B ILE* 5.3 9.9 - - + -
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Residues in contact with LEU 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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275B ILE* 3.9 29.6 - - + -
280B ALA* 4.1 11.9 - - + +
283B SER* 4.5 4.3 - - - +
348B ILE* 2.5 28.1 + - + +
349B MET* 3.4 15.5 - - + +
351B PHE* 1.3 110.4 - - + +
353B LEU* 1.3 56.8 + - - +
355B ARG* 3.1 26.3 - - - +
356B ALA* 3.2 12.3 + - - +
363B VAL* 4.2 20.3 - - + +
366B HIS* 4.1 28.3 - - + -
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Residues in contact with LEU 353 (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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6B PHE* 3.8 32.6 - - + -
8B LEU* 6.0 0.7 - - + -
147B ARG* 4.8 5.6 - - + -
148B PRO* 4.5 17.7 - - + +
150B LEU* 4.3 27.4 - - + -
273B LEU* 4.9 2.5 - - + -
349B MET* 3.4 26.5 - - + +
350B PRO* 3.8 12.6 - - + +
351B PHE 3.2 0.2 - - - -
352B LEU* 1.3 77.5 - - - +
354B GLU* 1.3 63.0 + - - +
355B ARG 3.2 0.2 - - - -
356B ALA* 3.8 5.5 - - - +
357B THR* 2.4 36.0 + - - -
363B VAL* 4.4 12.1 - - + -
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Residues in contact with GLU 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ARG* 2.4 53.6 + - - +
350B PRO 3.2 16.3 + - - +
351B PHE* 3.6 5.1 + - - +
352B LEU 3.4 0.2 - - - -
353B LEU* 1.3 82.4 - - - +
355B ARG* 1.3 61.2 + - - +
357B THR* 3.2 14.8 - - - -
358B VAL* 3.3 13.2 + - - +
485B ASN* 5.3 1.0 + - - +
487B PRO* 4.5 5.8 - - + -
488B LEU* 3.0 52.9 - - + +
491B ALA* 3.9 2.8 - - + +
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Residues in contact with ARG 355 (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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283B SER* 4.3 12.7 + - - -
351B PHE* 3.3 32.0 + - + +
352B LEU* 3.1 19.0 - - - +
354B GLU* 1.3 74.4 - - - +
356B ALA* 1.3 60.8 + - + +
357B THR 2.9 1.8 - - - -
358B VAL* 2.7 25.1 + - - +
359B ASN* 2.3 39.6 + - - +
361B LEU* 5.8 0.4 - - - +
363B VAL 5.5 1.0 + - - -
365B ARG 3.6 18.5 + - - -
366B HIS* 3.5 30.3 + - - +
367B GLY 4.1 15.8 + - - +
491B ALA* 3.5 26.8 - - + +
494B ILE* 5.1 19.3 - - + +
495B ILE* 5.6 2.7 - - + -
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Residues in contact with ALA 356 (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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6B PHE* 5.0 1.3 - - + -
121B THR* 3.1 3.5 + - - -
122B SER* 3.7 11.1 + - - +
352B LEU 3.2 15.2 + - - +
353B LEU* 3.8 5.2 - - - +
355B ARG* 1.3 83.7 - - + +
357B THR* 1.3 62.9 + - - +
359B ASN* 3.3 11.2 - - - +
360B GLY* 3.0 21.8 + - - -
361B LEU 3.7 16.0 - - - +
363B VAL* 3.8 26.9 - - + -
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Residues in contact with THR 357 (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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6B PHE* 3.7 8.8 - - - -
121B THR* 2.3 38.5 + - + +
122B SER* 4.6 0.4 - - - -
123B PRO* 3.9 16.8 - - + -
143B HIS 6.0 0.2 - - - +
144B PRO 5.4 2.5 - - - +
147B ARG* 3.2 39.0 + - - +
353B LEU 2.4 21.3 + - - -
354B GLU 3.2 11.4 - - - -
356B ALA* 1.3 79.2 - - - +
358B VAL* 1.3 61.8 + - + +
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Residues in contact with VAL 358 (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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121B THR* 4.5 0.5 + - - -
354B GLU 3.3 11.9 + - - +
355B ARG* 2.7 11.9 + - - +
357B THR* 1.3 83.8 - - + +
359B ASN* 1.3 60.9 + - - +
360B GLY 3.8 0.2 + - - -
376B LEU* 4.2 17.4 - - + +
473B ILE* 5.4 6.3 - - + -
488B LEU* 5.2 4.9 - - + -
491B ALA* 5.1 3.8 - - + -
492B LEU* 3.8 29.2 - - + -
495B ILE* 3.8 35.7 - - + -
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Residues in contact with ASN 359 (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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355B ARG* 2.3 65.5 + - - +
356B ALA* 3.3 3.8 - - - +
358B VAL* 1.3 77.4 - - + +
360B GLY* 1.3 59.9 + - - +
361B LEU* 2.9 51.7 + - + +
362B PRO 5.3 0.4 + - - -
365B ARG 5.3 0.8 + - - -
372B ALA* 3.6 34.2 - - + +
375B HIS* 4.0 2.8 - - - +
376B LEU* 3.9 15.4 - - - +
495B ILE* 5.7 7.5 - - + +
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Residues in contact with GLY 360 (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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10B ARG* 3.0 23.0 + - - -
112B GLU* 5.8 0.2 - - - +
121B THR* 3.2 32.2 + - - +
122B SER* 5.1 0.2 - - - -
356B ALA 3.0 9.7 + - - -
359B ASN* 1.3 77.7 - - - +
361B LEU* 1.3 63.5 + - - +
375B HIS* 3.9 23.4 + - - -
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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