Contacts of the helix formed by residues 395 - 408 (chain A) in PDB entry 6M04
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 TYR 395 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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391A PRO* 5.8 2.9 - - + -
392A LEU* 4.5 18.7 - - + +
393A LYS* 3.3 6.4 - - - +
394A GLU* 1.3 74.9 - - - +
396A SER* 1.3 58.9 + - - +
397A PHE* 3.1 2.9 - - - +
398A GLU* 2.9 37.0 + - + +
399A LYS* 3.0 13.5 + - - +
421A HIS* 5.3 2.2 - - - -
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Residues in contact with SER 396 (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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393A LYS 5.2 0.2 - - - -
394A GLU 3.2 3.3 - - - -
395A TYR* 1.3 75.4 - - - +
397A PHE* 1.3 58.9 + - - +
399A LYS* 3.3 23.8 - - - +
400A VAL* 2.9 36.6 + - - +
415A ASP* 4.4 5.6 - - - +
418A PHE* 4.0 37.6 - - - -
420A LEU* 4.2 2.1 - - - +
421A HIS* 3.9 23.8 - - - -
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Residues in contact with PHE 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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394A GLU 4.3 7.4 - - - +
395A TYR* 4.9 0.7 - - - -
396A SER* 1.3 75.0 - - - +
398A GLU* 1.3 56.5 + - - +
400A VAL* 5.0 0.2 - - - -
401A ARG* 2.9 25.4 + - - +
413A LYS 2.9 12.2 - - - +
414A ASN* 3.7 12.6 - - + +
415A ASP 3.2 40.7 + - - +
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Residues in contact with GLU 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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395A TYR* 2.9 27.6 + - + +
397A PHE* 1.3 79.9 - - - +
399A LYS* 1.3 65.7 + - - +
401A ARG* 3.3 7.5 + - + +
402A GLU* 2.9 34.8 + - - +
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Residues in contact with LYS 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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395A TYR 3.0 9.1 + - - +
396A SER* 3.3 33.9 - - - +
398A GLU* 1.3 83.3 - - - +
400A VAL* 1.3 70.8 + - + +
402A GLU* 3.3 6.9 + - - +
403A GLU* 2.9 28.0 + - - +
420A LEU* 3.4 26.6 + - - +
421A HIS* 4.3 17.3 - - + +
424A ASP* 4.5 15.1 + - - +
428A GLN* 5.7 1.6 - - - +
431A SER* 2.4 35.7 + - - +
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Residues in contact with VAL 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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396A SER* 2.9 24.4 + - - +
397A PHE* 4.2 2.5 - - - +
399A LYS* 1.3 95.0 - - - +
401A ARG* 1.3 56.5 + - - +
403A GLU* 3.4 20.5 - - - +
404A SER* 2.8 36.8 + - - +
411A ASP* 4.8 5.6 - - + -
413A LYS* 3.8 24.7 - - - +
414A ASN 4.8 1.3 - - - +
415A ASP* 5.6 6.1 - - + -
420A LEU* 4.5 10.1 - - + -
435A GLY* 5.2 5.4 - - - -
438A LEU* 4.7 17.3 - - + -
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Residues in contact with ARG 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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397A PHE 2.9 20.1 + - - +
398A GLU* 3.4 10.1 - - + +
399A LYS 3.2 0.2 - - - -
400A VAL* 1.3 74.3 - - - +
402A GLU* 1.3 59.7 + - - +
404A SER* 3.3 3.3 + - - -
405A SER* 2.8 32.1 + - - +
413A LYS* 3.5 23.3 + - + +
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Residues in contact with GLU 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 GLU* 2.9 26.7 + - - +
399A LYS* 3.7 7.6 - - - +
401A ARG* 1.3 72.5 - - - +
403A GLU* 1.3 62.0 + - - +
405A SER* 2.9 28.5 + - - -
406A PHE* 3.0 40.1 + - + +
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Residues in contact with GLU 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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399A LYS* 2.9 17.6 + - - +
400A VAL* 3.4 25.4 - - - +
402A GLU* 1.3 76.1 - - - +
404A SER* 1.3 52.1 + - - +
406A PHE* 3.6 15.1 + - + -
407A SER* 2.5 43.3 + - - -
411A ASP* 6.3 0.7 - - + -
420A LEU* 5.7 0.3 - - - +
428A GLN* 5.5 2.2 - - - +
431A SER* 3.1 25.3 + - - +
432A LYS* 3.0 49.7 - - + +
435A GLY* 3.3 16.5 - - - -
436A VAL* 3.9 0.5 + - - +
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Residues in contact with SER 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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400A VAL* 2.8 22.4 + - - +
401A ARG 3.6 5.2 - - - -
403A GLU* 1.3 72.4 - - - +
405A SER* 1.3 64.0 + - - +
407A SER* 3.5 13.6 + - - -
408A ASP* 4.2 5.0 + - - -
409A ILE 4.6 0.2 - - - -
410A PRO* 4.1 17.8 - - - +
411A ASP* 3.0 41.9 + - - +
413A LYS* 3.7 14.6 - - - +
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Residues in contact with SER 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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401A ARG* 2.8 19.8 + - - +
402A GLU* 2.9 23.7 + - - -
404A SER* 1.3 79.0 - - - +
406A PHE* 1.3 57.2 + - - +
408A ASP 5.0 1.4 + - - -
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Residues in contact with PHE 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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402A GLU* 3.0 53.5 + - + +
403A GLU* 3.8 12.3 - - + -
405A SER* 1.3 74.9 - - - +
407A SER* 1.3 64.4 + - - +
408A ASP* 3.4 4.9 + - - +
428A GLN* 6.2 4.5 - - + -
432A LYS* 3.3 39.5 - - - -
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Residues in contact with SER 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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213A LEU* 6.1 0.9 - - - +
216A THR* 4.8 2.1 - - - +
403A GLU* 2.5 29.7 + - - +
404A SER* 3.5 8.0 + - - -
405A SER 3.5 1.6 - - - -
406A PHE* 1.3 81.0 - - - +
408A ASP* 1.3 64.1 + - - +
409A ILE* 3.1 29.7 + - - +
432A LYS* 4.8 7.7 - - - +
435A GLY 6.0 0.2 - - - -
436A VAL* 4.1 21.7 - - - +
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Residues in contact with ASP 408 (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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216A THR* 3.6 24.9 - - + +
404A SER 4.2 4.4 + - - -
405A SER 5.0 1.4 + - - -
406A PHE 3.4 4.3 - - - +
407A SER* 1.3 76.1 - - - +
409A ILE* 1.3 61.7 + - - +
410A PRO* 3.8 9.8 - - - +
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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