Contacts of the helix formed by residues 390 - 405 (chain A) in PDB entry 3M6L
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 ARG 390 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A GLU* 3.5 54.2 + - + +
165A SER* 2.9 30.3 + - - -
166A LEU* 3.5 30.2 - - + +
169A LEU* 5.3 7.1 - - - +
363A ALA* 4.1 4.3 - - - +
386A HIS 4.8 0.6 + - - -
387A PHE 2.8 40.6 + - - +
388A GLY* 3.0 12.7 + - - -
389A ILE* 1.3 79.1 - - - +
391A GLU* 1.4 66.1 + - - +
392A HIS 3.3 3.1 - - - -
393A ALA* 3.5 3.8 + - + -
394A MSE 2.9 22.3 + - - +
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Residues in contact with GLU 391 (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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162A GLU* 4.9 1.1 + - - +
363A ALA* 3.9 18.7 - - + +
365A LEU* 5.7 1.4 - - - +
389A ILE* 4.1 20.0 - - - +
390A ARG* 1.4 78.4 + - - +
392A HIS* 1.3 63.4 + - - +
394A MSE 3.4 10.4 + - - +
395A ALA 3.2 17.7 + - - -
413A THR* 3.9 23.8 + - - +
417A PHE* 4.1 23.7 - - - +
420A TYR* 3.7 38.7 - - + -
421A LEU* 3.4 19.6 - - + +
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Residues in contact with HIS 392 (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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118A GLN* 2.9 34.0 + - - -
159A ILE* 3.6 27.9 - - + +
162A GLU* 3.7 13.0 + - - +
390A ARG 3.3 0.8 - - - -
391A GLU* 1.3 78.2 + - - +
393A ALA* 1.3 63.0 + - - +
395A ALA* 3.2 3.8 + - - +
396A ALA 3.1 18.2 + - - -
420A TYR* 3.3 23.5 + - + +
421A LEU* 4.0 5.7 - - - -
423A PRO* 3.6 30.9 - - + +
424A ALA* 3.8 10.1 - - - +
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Residues in contact with ALA 393 (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 ALA* 4.5 2.0 - - - -
159A ILE* 3.7 13.6 - - + +
162A GLU* 2.9 39.8 + - + +
163A ALA* 3.8 19.5 - - + +
166A LEU* 5.2 0.4 - - + -
390A ARG* 4.2 6.5 - - + +
392A HIS* 1.3 73.0 - - - +
394A MSE 1.3 60.4 + - - +
396A ALA* 3.7 0.6 - - - +
397A ILE* 2.8 41.5 + - + +
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Residues in contact with MSE 394 (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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166A LEU* 5.6 0.2 - - - +
361A GLY 3.8 2.5 - - - +
363A ALA* 3.6 29.2 - - + -
387A PHE* 3.5 53.0 - - + -
390A ARG* 2.9 19.4 + - - +
391A GLU* 3.6 7.2 - - + +
392A HIS 3.2 0.2 - - - -
393A ALA* 1.3 76.1 - - - +
395A ALA* 1.4 57.1 + - - +
397A ILE* 3.4 1.8 + - - +
398A ASN* 3.0 29.3 + - - +
411A SER* 3.8 10.8 - - - +
412A ALA 3.5 37.5 - - - +
413A THR* 4.5 1.1 - - - -
421A LEU* 3.7 29.4 - - + -
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Residues in contact with ALA 395 (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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391A GLU 3.2 3.8 + - - +
392A HIS 3.2 4.0 + - - +
394A MSE 1.4 77.4 - - - +
396A ALA* 1.3 57.4 + - - +
399A ASN* 2.9 28.1 + - - -
411A SER* 3.9 10.1 - - - +
421A LEU* 3.8 24.2 - - + +
424A ALA* 3.6 21.3 - - + -
435A HIS* 3.3 8.9 - - + -
437A PHE* 4.1 21.1 - - + -
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Residues in contact with ALA 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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118A GLN* 3.7 21.8 - - - +
121A ALA* 3.6 27.1 - - + -
122A ASN* 2.9 31.2 - - - +
159A ILE* 3.9 2.5 - - + -
392A HIS 3.1 15.5 + - - +
393A ALA 3.9 0.2 - - - +
395A ALA* 1.3 74.7 - - - +
397A ILE* 1.3 65.5 + - - +
399A ASN* 3.4 3.9 + - - +
400A ALA 3.3 12.6 + - - -
424A ALA* 3.7 4.7 - - + +
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Residues in contact with ILE 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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121A ALA* 3.6 19.1 - - + +
124A VAL* 4.2 9.6 - - + -
125A GLY* 3.8 17.0 - - - +
128A MSE 4.1 15.5 - - - -
163A ALA* 4.8 2.5 - - + -
166A LEU* 3.6 31.9 - - + -
387A PHE* 3.9 16.6 - - + -
393A ALA* 2.8 31.0 + - + +
394A MSE 3.7 2.5 - - - +
396A ALA* 1.3 73.8 - - - +
398A ASN* 1.3 57.9 + - - +
400A ALA* 3.1 7.8 + - - +
401A PHE* 2.9 48.4 + - + -
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Residues in contact with ASN 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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360A GLY* 5.1 1.4 - - - -
385A ILE* 4.6 5.1 - - - +
387A PHE* 3.5 25.9 - - - -
394A MSE 3.0 15.4 + - - +
397A ILE* 1.3 74.5 - - - +
399A ASN* 1.3 63.3 + - - +
401A PHE* 3.3 17.3 + - - -
402A ALA* 3.0 20.1 + - - +
409A PRO* 3.5 29.7 - - + +
410A PHE 2.9 17.6 + - - +
411A SER* 2.8 17.4 + - - -
435A HIS* 3.3 24.6 + - + +
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Residues in contact with ASN 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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111A ILE* 4.1 3.1 - - + -
118A GLN* 5.0 0.8 + - - -
122A ASN* 4.2 7.4 + - - +
395A ALA 2.9 17.8 + - - -
396A ALA* 3.4 11.1 - - - +
397A ILE 3.3 0.2 - - - -
398A ASN* 1.3 73.3 - - - +
400A ALA* 1.3 62.0 + - - +
402A ALA* 3.3 5.0 + - - +
403A ARG* 3.2 25.1 + - - +
424A ALA* 3.0 33.4 + - - +
427A ILE* 3.8 11.5 - - - +
428A ALA* 3.4 19.7 - - - +
431A MSE 4.1 8.7 - - + -
433A ILE* 3.4 14.9 - - + +
435A HIS* 2.8 22.3 + - - -
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Residues in contact with ALA 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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111A ILE* 4.0 5.6 - - - +
122A ASN* 3.1 35.9 - - - +
125A GLY* 3.7 2.0 - - - -
126A PHE* 3.4 35.8 - - + +
396A ALA 3.3 2.0 + - - -
397A ILE 3.1 9.9 + - - +
399A ASN* 1.3 78.0 - - - +
401A PHE* 1.3 68.0 + - - +
403A ARG 3.0 1.6 + - - -
404A TYR* 2.9 20.3 + - - +
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Residues in contact with PHE 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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125A GLY 3.9 6.9 + - - -
128A MSE 3.8 22.2 - - + -
129A ALA* 3.6 35.4 - - + -
132A LYS* 4.5 4.0 - - + -
359A LEU* 4.0 26.9 - - + -
379A PHE* 4.0 12.1 - + - -
385A ILE* 4.1 12.1 - - + -
397A ILE* 2.9 44.5 + - + -
398A ASN* 3.6 20.0 - - - +
400A ALA* 1.3 74.8 - - - +
402A ALA* 1.3 61.4 + - - +
404A TYR* 3.2 12.3 + - - +
407A PHE* 3.5 40.2 + + + +
409A PRO* 4.0 14.4 - - + -
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Residues in contact with ALA 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 ASN 3.0 13.2 + - - +
399A ASN 3.5 9.9 - - - +
400A ALA 3.2 0.2 - - - -
401A PHE* 1.3 75.4 - - - +
403A ARG* 1.3 62.0 + - - +
405A GLY* 4.7 3.7 + - - -
407A PHE 4.2 8.2 + - - +
409A PRO* 3.9 11.8 - - + +
433A ILE* 3.6 26.2 - - + +
434A LYS 3.6 24.0 + - - +
435A HIS* 4.3 1.3 - - + -
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Residues in contact with ARG 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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58A ARG* 4.8 11.8 + - - +
104A ILE* 3.5 34.0 + - - +
109A VAL 3.3 17.2 + - - -
110A GLU* 3.0 30.5 + - - +
111A ILE* 4.3 4.5 - - + -
126A PHE* 3.7 17.7 - - + -
399A ASN 3.2 15.0 + - - +
400A ALA 3.0 8.3 + - - +
402A ALA* 1.3 76.8 - - - +
404A TYR* 1.3 64.6 + - - +
405A GLY* 3.4 3.9 + - - -
431A MSE 4.1 20.4 - - + -
433A ILE* 3.7 21.7 - - + +
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Residues in contact with TYR 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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56A LEU* 3.8 18.0 + - + +
58A ARG* 4.9 3.8 + - - -
60A ARG* 3.0 46.8 + - + +
126A PHE* 3.8 22.2 - + - -
129A ALA* 3.7 20.9 - - + -
130A ALA* 3.6 23.6 - - - -
133A ALA* 3.7 18.1 - - + +
142A ILE* 3.7 12.8 - - - +
144A HIS* 2.6 38.2 + + - -
400A ALA 2.9 10.1 + - - +
401A PHE 3.2 13.5 + - - +
403A ARG* 1.3 79.7 - - - +
405A GLY* 1.3 58.9 + - - +
406A ILE* 4.2 6.7 - - + -
407A PHE* 3.9 15.0 - + + -
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Residues in contact with GLY 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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56A LEU* 4.2 7.0 - - - -
320A LEU 4.9 1.4 - - - +
321A LEU* 3.6 16.3 - - - +
401A PHE 4.4 1.6 + - - -
402A ALA 4.7 3.4 + - - -
403A ARG 3.4 4.1 - - - -
404A TYR* 1.3 80.4 - - - +
406A ILE* 1.3 69.5 + - - +
407A PHE 3.9 1.1 - - - +
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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