Contacts of the helix formed by residues 416 - 429 (chain A) in PDB entry 6ML4
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 ASP 416 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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405A PRO* 3.7 12.8 - - - +
414A PHE* 3.3 1.8 - - - +
415A MET* 1.3 81.4 - - - +
417A VAL* 1.3 64.7 + - - +
418A SER* 2.9 32.7 + - - -
419A GLN* 3.0 35.6 + - - +
420A LEU* 3.1 19.6 + - - +
15E C 4.2 3.6 + - - -
5F T 3.7 27.6 - - + +
6F C 3.1 21.3 + - - -
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Residues in contact with VAL 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A PRO* 3.9 19.5 - - + -
416A ASP* 1.3 75.6 - - + +
418A SER* 1.3 59.7 + - - +
420A LEU* 3.3 10.8 + - + +
421A LYS* 2.9 45.2 + - - +
5F T 3.4 58.0 + - + +
6F C 3.8 3.6 - - - +
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Residues in contact with SER 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A ASP* 2.9 12.2 + - - -
417A VAL* 1.3 79.7 - - - +
419A GLN* 1.3 66.4 + - - +
421A LYS* 3.3 6.4 + - - +
422A LYS* 3.0 28.6 + - - +
5F T 4.2 0.9 - - - -
6F C 3.4 57.0 + - - +
7F G 4.4 7.6 + - - -
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Residues in contact with GLN 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A PHE* 4.1 19.5 - - + -
415A MET* 4.5 8.7 - - + +
416A ASP* 3.0 43.4 + - - +
418A SER* 1.3 79.0 + - - +
420A LEU* 1.3 62.0 + - - +
422A LYS* 3.3 25.8 + - - +
423A HIS* 3.0 22.3 + - - +
12E G 5.9 3.1 - - + +
13E G 4.5 11.1 - - + +
14E A 3.1 22.8 + - - +
15E C 3.6 3.4 - - - +
6F C 3.6 6.5 - - - +
7F G 2.8 26.5 + - - +
8F T 3.9 0.5 - - - +
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Residues in contact with LEU 420 (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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405A PRO* 3.5 25.1 - - + +
406A GLU 3.4 34.3 - - - +
407A CYS* 3.6 10.1 - - + +
414A PHE* 4.0 16.7 - - + +
416A ASP 3.1 12.5 + - - +
417A VAL* 3.5 13.7 - - + +
418A SER 3.2 0.2 - - - -
419A GLN* 1.3 77.9 - - - +
421A LYS* 1.3 61.7 + - + +
423A HIS* 3.0 5.2 + - - +
424A LEU* 2.9 52.4 + - + +
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Residues in contact with LYS 421 (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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417A VAL* 2.9 32.5 + - + +
418A SER* 3.3 5.6 + - - +
420A LEU* 1.3 78.8 - - + +
422A LYS* 1.3 63.7 + - - +
424A LEU* 3.3 31.6 + - + +
425A ARG* 3.9 12.5 + - - +
5F T 4.4 1.8 + - - -
6F C 3.2 37.5 + - - +
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Residues in contact with LYS 422 (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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418A SER* 3.0 19.2 + - - +
419A GLN* 3.3 28.1 + - - +
420A LEU 3.3 0.2 - - - -
421A LYS* 1.3 77.6 - - - +
423A HIS* 1.3 61.8 + - - +
425A ARG* 3.3 50.8 + - - +
426A THR* 4.4 2.8 + - - +
444A ALA* 6.0 4.3 - - + -
12E G 3.9 21.2 + - + -
13E G 3.1 18.0 + - - -
7F G 5.7 1.3 - - - +
8F T 2.8 41.8 + - + +
9F C 4.2 2.8 - - - +
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Residues in contact with HIS 423 (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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407A CYS* 3.7 10.1 - - + -
410A CYS* 3.2 3.0 - - - -
412A ARG* 3.1 29.4 - - - -
414A PHE* 3.1 37.8 - + + -
419A GLN 3.0 12.7 + - - +
420A LEU* 3.0 8.7 + - - +
422A LYS* 1.3 75.0 - - - +
424A LEU* 1.3 63.1 + - - +
426A THR* 2.6 44.8 + - - -
427A HIS* 3.1 2.4 + - - -
602A ZN 2.0 37.0 - - - -
12E G 2.9 26.8 + - - +
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Residues in contact with LEU 424 (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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407A CYS* 4.0 26.2 - - - -
408A SER* 5.6 4.0 - - - +
409A HIS* 5.8 1.3 - - + -
420A LEU* 2.9 33.3 + - + +
421A LYS* 3.4 24.5 - - + +
422A LYS 3.2 0.4 - - - -
423A HIS* 1.3 77.7 - - - +
425A ARG* 1.3 56.6 + - + +
427A HIS* 3.0 26.1 + - + +
428A THR* 3.3 19.2 + - + +
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Residues in contact with ARG 425 (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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421A LYS* 4.3 8.4 + - - +
422A LYS* 3.6 47.6 + - - +
423A HIS 3.1 1.2 - - - -
424A LEU* 1.3 76.9 - - + +
426A THR* 1.3 56.6 + - - +
427A HIS 3.1 0.2 - - - -
428A THR* 3.5 8.1 - - - +
429A GLY* 2.9 28.9 + - - -
430A GLU* 3.5 47.2 + - - +
432A PRO* 3.7 17.4 - - - +
433A PHE* 4.2 11.1 - - - -
443A THR* 3.1 35.2 + - - +
444A ALA* 4.8 3.6 - - - +
11E T 4.9 2.9 + - - +
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Residues in contact with THR 426 (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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412A ARG* 4.9 1.6 + - - -
422A LYS 4.8 2.2 - - - +
423A HIS* 2.6 40.2 + - - +
425A ARG* 1.3 77.5 - - - +
427A HIS* 1.3 66.5 + - - +
429A GLY* 4.4 2.5 + - - -
11E T 3.4 48.2 + - + +
12E G 3.7 18.8 - - - +
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Residues in contact with HIS 427 (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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407A CYS* 3.6 4.2 - - - -
409A HIS* 3.5 52.0 + + + +
410A CYS* 3.9 9.9 - - + -
412A ARG* 5.0 4.0 - - - -
423A HIS* 3.1 11.9 + + - -
424A LEU* 3.0 16.0 + - + +
426A THR* 1.3 87.9 + - - +
428A THR* 1.3 63.5 + - + +
429A GLY 3.5 0.2 - - - -
602A ZN 2.0 37.5 - - - -
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Residues in contact with THR 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A LEU* 3.3 16.1 + - + +
425A ARG* 3.5 9.9 - - - -
427A HIS* 1.3 81.7 - - + +
429A GLY* 1.3 62.4 + - - +
430A GLU* 3.2 25.2 + - - +
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Residues in contact with GLY 429 (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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425A ARG 2.9 12.3 + - - -
426A THR 4.4 2.5 + - - -
427A HIS 3.5 2.0 - - - -
428A THR* 1.3 77.2 - - - +
430A GLU* 1.3 64.4 + - - +
431A LYS* 3.4 18.5 + - - +
443A THR* 6.1 0.7 - - - -
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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