Contacts of the helix formed by residues 396 - 407 (chain A) in PDB entry 3KMU
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 SER 396 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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395A LEU* 1.3 74.7 - - - +
397A ASN* 1.3 59.4 + - - +
398A MSE 3.8 3.1 + - - -
399A GLU* 2.7 39.9 + - - +
400A ILE* 2.9 26.0 + - - +
278B LYS* 5.7 4.5 - - - -
301B GLY 6.1 0.4 - - - -
302B LEU* 4.1 18.1 - - - +
305B GLY* 5.9 4.7 - - - -
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Residues in contact with ASN 397 (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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351A TYR* 2.9 31.7 + - - +
352A ALA* 4.6 0.5 - - - -
353A PRO* 3.2 30.0 - - + +
395A LEU 4.0 0.4 + - - +
396A SER* 1.3 72.2 - - - +
398A MSE 1.3 63.3 + - - +
400A ILE* 3.1 11.8 + - - +
401A GLY 3.0 20.3 + - - -
305B GLY* 2.8 30.9 + - - +
306B TYR* 3.8 10.3 - - - -
307B PHE* 3.6 7.5 - - - +
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Residues in contact with MSE 398 (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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396A SER* 3.3 2.3 + - - +
397A ASN* 1.3 77.5 - - - +
399A GLU* 1.3 65.0 + - - +
401A GLY 3.5 0.2 + - - -
402A MSE 2.8 74.9 + - + +
279B LEU* 3.8 21.5 - - + -
298B LEU* 3.7 25.6 - - + +
301B GLY* 4.2 8.0 + - - +
302B LEU* 3.8 26.9 - - + -
305B GLY 5.3 0.2 - - - -
306B TYR 3.6 16.0 + - - +
307B PHE* 3.2 30.1 - - + +
308B VAL* 4.1 9.9 - - - +
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Residues in contact with GLU 399 (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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394A ASP 5.1 0.9 - - - +
395A LEU* 3.6 25.7 - - + +
396A SER* 2.7 41.5 + - - +
398A MSE 1.3 79.4 - - - +
400A ILE* 1.3 63.1 + - - +
402A MSE 4.0 0.3 - - - +
403A LYS* 3.0 41.2 + - - +
278B LYS* 3.8 52.2 + - + +
279B LEU* 4.0 12.3 - - + -
302B LEU* 4.8 1.1 - - + -
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Residues in contact with ILE 400 (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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353A PRO* 4.0 6.5 - - + +
354A ALA* 3.8 38.8 - - + +
391A PRO 4.5 1.3 - - - +
392A PHE* 3.7 41.1 - - + +
395A LEU* 3.6 31.9 - - + +
396A SER 2.9 14.2 + - - +
397A ASN* 3.1 21.5 + - - +
399A GLU* 1.3 77.4 - - - +
401A GLY* 1.3 65.2 + - - +
403A LYS* 3.8 0.5 - - - +
404A VAL* 2.9 36.9 + - + +
409A LEU* 4.9 1.6 - - - -
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Residues in contact with GLY 401 (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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353A PRO* 4.2 5.6 - - - +
361A LEU* 3.6 12.8 - - - +
397A ASN 3.0 11.3 + - - -
400A ILE* 1.3 78.6 - - - +
402A MSE 1.3 57.7 + - - +
405A ALA* 3.0 34.0 + - - +
307B PHE* 3.3 32.5 - - - -
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Residues in contact with MSE 402 (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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398A MSE 2.8 53.2 + - + +
399A GLU 4.0 1.8 - - - +
401A GLY* 1.3 76.0 - - - +
403A LYS* 1.3 59.4 + - + +
406A LEU* 2.8 79.0 + - + +
407A GLU* 4.8 2.4 - - - +
279B LEU* 3.9 24.5 - - + -
298B LEU* 4.2 11.0 - - - -
307B PHE* 3.4 8.4 - - + -
310B LEU* 3.6 26.7 - - + -
315B LEU* 4.6 4.7 - - + -
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Residues in contact with LYS 403 (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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395A LEU* 4.1 21.3 - - + -
399A GLU* 3.0 39.3 + - - +
402A MSE 1.3 76.4 - - + +
404A VAL* 1.3 61.0 + - - +
407A GLU* 2.9 58.1 + - + +
408A GLY 3.1 0.2 + - - -
409A LEU* 3.0 35.6 + - + -
278B LYS 3.5 23.5 + - - -
279B LEU* 5.0 4.7 - - + +
280B ASN* 4.3 11.1 + - - +
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Residues in contact with VAL 404 (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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353A PRO 5.6 2.0 - - - +
354A ALA* 5.8 0.9 - - - +
356A VAL 4.8 4.5 - - - +
358A PRO* 4.1 18.1 - - + +
361A LEU* 3.6 21.1 - - + -
376A TRP* 5.3 4.0 - - + +
392A PHE* 4.1 14.6 - - + -
400A ILE* 2.9 40.5 + - + +
403A LYS* 1.3 73.5 - - - +
405A ALA* 1.3 62.0 + - - +
408A GLY 3.8 3.8 + - - -
409A LEU* 3.5 25.6 - - + +
410A ARG* 2.9 37.5 + - - +
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Residues in contact with ALA 405 (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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358A PRO* 4.8 1.3 - - - -
361A LEU* 3.8 12.8 - - + +
362A GLN* 3.7 48.6 + - + +
401A GLY 3.0 19.7 + - - +
402A MSE 4.0 1.8 - - - +
404A VAL* 1.3 79.6 - - - +
406A LEU* 1.3 68.8 + - + +
408A GLY 4.9 0.6 + - - -
307B PHE* 4.8 1.6 - - + -
310B LEU* 4.3 7.2 - - + -
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Residues in contact with LEU 406 (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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362A GLN* 4.4 6.7 - - - +
402A MSE 2.8 50.8 + - + +
405A ALA* 1.3 79.9 - - - +
407A GLU* 1.3 63.4 + - + +
408A GLY 3.7 0.9 - - - -
310B LEU* 3.8 20.4 - - + -
315B LEU* 4.0 18.2 - - + -
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Residues in contact with GLU 407 (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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402A MSE 5.2 1.9 - - - +
403A LYS* 2.9 50.0 + - + +
406A LEU* 1.3 83.6 - - + +
408A GLY* 1.3 63.2 + - - +
409A LEU* 4.6 1.5 - - + +
279B LEU 5.1 5.4 - - - +
280B ASN* 4.5 10.1 - - - +
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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