Contacts of the helix formed by residues 347 - 360 (chain A) in PDB entry 3K57
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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343A PHE 3.0 6.2 + - - -
344A HIS* 3.0 17.1 + - - +
345A LYS 3.8 6.7 - - - +
346A THR* 1.3 79.9 - - - +
348A ILE* 1.3 63.3 + - - +
349A MET 3.4 2.5 - - - -
350A PRO* 3.2 21.7 - - + +
351A PHE* 3.2 19.9 + - - +
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Residues in contact with ILE 348 (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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280A ALA* 3.6 42.4 - - + +
281A LEU* 4.1 10.8 - - + -
284A ALA* 3.7 22.4 - - + -
286A TRP* 4.8 3.6 - - - +
343A PHE* 3.2 52.1 + - + +
346A THR* 3.0 14.2 - - - +
347A GLU* 1.3 75.3 - - - +
349A MET* 1.3 64.7 + - - +
351A PHE* 3.2 14.4 + - + +
352A LEU* 2.9 30.6 + - + +
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Residues in contact with MET 349 (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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150A LEU* 4.5 21.5 - - + -
152A TRP* 3.3 37.2 - - + +
219A VAL* 4.4 16.6 - - + -
273A LEU* 4.5 13.2 - - + -
275A ILE* 4.1 22.2 - - + -
343A PHE* 3.9 21.7 + - + -
348A ILE* 1.3 78.3 - - - +
350A PRO* 1.3 75.2 - - + +
352A LEU* 3.1 10.8 + - + +
353A LEU* 2.9 33.2 + - + +
363A VAL* 4.6 10.3 - - + -
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Residues in contact with PRO 350 (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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152A TRP* 5.6 2.0 - - + -
343A PHE 5.7 0.2 - - - +
347A GLU* 3.2 26.7 - - + +
349A MET* 1.3 95.3 - - + +
351A PHE* 1.3 61.1 + - - +
353A LEU* 3.3 13.2 + - + +
354A GLU* 2.9 32.6 + - + +
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Residues in contact with PHE 351 (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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283A SER* 3.7 11.7 - - - -
284A ALA* 3.6 32.5 - - + -
346A THR 5.5 1.1 - - - +
347A GLU 3.2 11.5 + - - +
348A ILE* 3.2 21.5 + - + +
349A MET 3.1 0.2 - - - -
350A PRO* 1.3 80.3 - - - +
352A LEU* 1.3 68.3 + - + +
354A GLU* 3.3 5.1 + - - +
355A ARG* 2.8 60.0 + - - +
485A ASN* 5.4 6.7 - - - +
487A PRO* 3.7 18.2 - - + -
488A LEU* 4.0 23.9 - - + +
491A ALA* 3.6 29.2 - - + -
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Residues in contact with LEU 352 (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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275A ILE* 4.0 38.8 - - + -
280A ALA* 4.2 9.4 - - + -
283A SER* 3.9 6.5 - - - +
348A ILE* 2.9 25.2 + - + +
349A MET* 3.1 13.0 + - + +
351A PHE* 1.3 90.5 - - + +
353A LEU* 1.3 66.2 + - - +
355A ARG* 3.6 33.4 + - - +
356A ALA* 3.0 26.0 + - - +
363A VAL* 3.8 23.1 - - + +
366A HIS* 3.9 7.2 - - + -
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Residues in contact with LEU 353 (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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6A PHE* 3.5 40.5 - - + -
8A LEU* 5.9 0.4 - - + -
147A ARG* 4.7 13.5 - - + -
148A PRO* 4.4 18.8 - - + +
150A LEU* 4.3 28.9 - - + -
273A LEU* 5.3 1.6 - - + -
349A MET* 2.9 26.8 + - + +
350A PRO* 3.7 13.2 - - + +
352A LEU* 1.3 77.6 - - - +
354A GLU* 1.3 62.1 + - - +
356A ALA* 3.5 2.2 + - - +
357A THR* 2.8 29.3 + - - -
363A VAL* 4.2 13.2 - - + -
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Residues in contact with GLU 354 (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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147A ARG* 2.9 45.7 + - - +
350A PRO* 2.9 23.0 + - + +
351A PHE* 3.7 4.5 - - - +
353A LEU* 1.3 77.6 - - - +
355A ARG* 1.3 62.5 + - - +
357A THR* 3.3 5.6 + - - -
358A VAL* 3.2 27.7 + - + +
485A ASN* 5.6 2.5 - - - +
488A LEU* 3.8 32.4 - - + +
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Residues in contact with ARG 355 (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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283A SER* 2.6 38.5 + - - -
351A PHE* 2.8 40.2 + - + +
352A LEU* 3.6 16.9 + - - +
354A GLU* 1.3 76.0 - - - +
356A ALA* 1.3 61.0 + - - +
358A VAL* 3.2 7.3 + - - +
359A ASN* 2.9 43.9 + - - +
363A VAL 4.5 3.4 + - - -
365A ARG 3.3 17.2 + - - -
366A HIS* 2.7 35.7 + - - +
367A GLY 5.2 2.9 + - - +
488A LEU* 4.6 8.2 - - + +
491A ALA* 4.9 7.9 - - + -
492A LEU* 5.6 1.1 - - + -
495A ILE* 4.3 18.6 - - + -
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Residues in contact with ALA 356 (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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121A THR* 3.7 2.8 - - - -
122A SER* 3.9 9.7 + - - +
352A LEU 3.0 17.9 + - - +
353A LEU 3.9 2.2 - - - +
355A ARG* 1.3 75.9 - - - +
357A THR* 1.3 66.8 + - - +
359A ASN* 3.4 10.1 - - - -
360A GLY* 2.9 25.5 + - - -
361A LEU 3.5 17.7 - - - +
362A PRO 4.4 0.7 - - - +
363A VAL* 3.8 27.1 - - + -
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Residues in contact with THR 357 (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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6A PHE* 3.5 19.4 - - - -
121A THR* 2.8 32.7 + - - +
122A SER* 4.6 0.6 + - - +
123A PRO* 3.6 27.0 - - + +
143A HIS 5.9 0.4 - - - +
144A PRO 6.0 0.9 - - - +
147A ARG* 3.8 22.1 - - - +
353A LEU 2.8 21.9 + - - -
354A GLU* 3.6 6.5 - - - -
355A ARG 3.2 0.2 - - - -
356A ALA* 1.3 75.3 - - - +
358A VAL* 1.3 58.3 + - + +
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Residues in contact with VAL 358 (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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121A THR* 4.4 0.5 - - - +
354A GLU* 3.2 14.0 + - + +
355A ARG 3.2 7.7 + - - +
356A ALA 3.1 0.6 - - - -
357A THR* 1.3 81.9 - - + +
359A ASN* 1.3 62.4 + - - +
376A LEU* 3.5 22.3 - - - +
473A ILE* 4.0 29.8 - - + -
476A GLY* 6.2 1.6 - - - -
488A LEU* 6.0 0.4 - - + -
492A LEU* 3.8 36.6 - - + -
495A ILE* 4.4 8.7 - - + -
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Residues in contact with ASN 359 (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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355A ARG* 2.9 42.0 + - - +
356A ALA* 3.4 8.4 - - - +
358A VAL* 1.3 73.6 - - - +
360A GLY* 1.3 58.5 + - - +
361A LEU* 2.9 40.4 + - - +
362A PRO 5.4 0.2 - - - +
365A ARG 5.0 3.0 + - - -
367A GLY 4.4 5.7 + - - -
372A ALA* 3.4 38.5 - - + +
375A HIS* 4.2 3.3 - - - +
376A LEU* 4.4 8.2 - - + +
495A ILE* 4.3 20.7 - - + +
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Residues in contact with GLY 360 (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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10A ARG* 4.5 10.5 + - - -
121A THR* 3.7 26.0 - - - +
356A ALA 2.9 12.2 + - - -
358A VAL 3.5 2.8 + - - -
359A ASN* 1.3 75.8 - - - +
361A LEU* 1.3 62.7 + - - +
362A PRO* 4.6 0.9 - - - +
375A HIS* 3.5 35.1 + - - -
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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