Contacts of the helix formed by residues 3363 - 3376 (chain G) in PDB entry 1MZN
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 ASP3363 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3315G HIS* 3.8 4.0 - - - -
3361G GLN 3.2 3.0 + - - +
3362G MET* 1.3 76.7 - - - +
3364G LYS* 1.3 58.0 + - - +
3365G THR* 2.9 8.0 + - - -
3366G GLU* 2.7 37.4 + - - +
3367G LEU* 3.0 23.9 + - - +
3403G TYR* 2.6 31.3 + - - -
3407G LYS* 4.8 0.7 - - - -
3408G TYR* 2.6 25.8 + - - +
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Residues in contact with LYS3364 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1237C GLU* 2.8 32.2 + - - +
3236G LEU* 3.7 17.2 - - + +
3239G GLU* 4.0 13.2 - - + +
3240G LEU* 4.0 18.2 - - + -
3243G GLU* 2.8 28.9 + - - +
3315G HIS* 3.9 20.2 - - + +
3363G ASP* 1.3 72.1 - - - +
3365G THR* 1.3 61.3 + - - +
3367G LEU* 3.8 10.2 - - + +
3368G GLY* 2.9 24.3 + - - -
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Residues in contact with THR3365 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1233C GLU* 4.4 9.7 - - - +
3232G VAL* 3.9 29.6 - - + +
3235G ILE* 4.4 1.6 - - + +
3236G LEU* 3.6 28.6 - - - +
3363G ASP* 2.9 9.6 + - - -
3364G LYS* 1.3 78.1 - - - +
3366G GLU* 1.3 59.1 + - - +
3368G GLY* 3.3 2.1 + - - -
3369G CYS* 3.0 32.2 + - - -
3403G TYR* 3.7 38.3 + - + -
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Residues in contact with GLU3366 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3362G MET* 3.6 11.1 - - + +
3363G ASP* 2.7 48.2 + - - +
3365G THR* 1.3 71.2 - - - +
3367G LEU* 1.3 64.3 + - - +
3369G CYS* 3.3 2.6 + - - +
3370G LEU* 3.0 29.6 + - - +
3400G LEU* 4.0 9.7 - - + +
3403G TYR* 3.6 15.7 - - + -
3404G CYS* 3.6 10.4 - - - -
3408G TYR* 3.3 8.5 - - - -
3414G ARG* 2.7 42.3 + - - -
3418G LEU* 3.7 22.2 - - + +
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Residues in contact with LEU3367 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3239G GLU* 3.9 16.2 - - - +
3311G ALA* 3.6 34.3 - - + +
3312G SER* 4.6 7.2 - - - +
3315G HIS* 3.4 35.4 - - + +
3357G MET* 3.9 19.1 - - + -
3362G MET* 4.1 9.1 - - - +
3363G ASP 3.0 16.3 + - - +
3364G LYS* 3.8 9.2 - - + +
3366G GLU* 1.3 75.2 - - - +
3368G GLY* 1.3 64.1 + - - +
3370G LEU* 3.3 6.0 + - + +
3371G ARG* 3.0 36.4 + - + +
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Residues in contact with GLY3368 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3235G ILE* 3.3 16.3 - - - +
3239G GLU* 3.4 33.2 - - - +
3282G TRP* 4.4 2.1 - - - -
3364G LYS 2.9 11.1 + - - -
3365G THR 3.6 1.6 - - - -
3367G LEU* 1.3 77.9 - - - +
3369G CYS* 1.3 56.3 + - - +
3371G ARG* 3.3 2.9 + - - +
3372G ALA* 2.9 28.6 + - - +
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Residues in contact with CYS3369 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3232G VAL* 4.1 18.6 - - - -
3235G ILE* 3.8 25.1 - - - -
3365G THR* 3.0 22.3 + - - +
3366G GLU 3.3 0.6 + - - +
3368G GLY* 1.3 76.4 - - - +
3370G LEU* 1.3 56.3 + - - +
3372G ALA 3.2 0.3 + - - -
3373G ILE* 2.9 34.0 + - - +
3396G VAL* 3.4 12.5 - - + +
3399G SER* 5.6 0.2 - - - -
3400G LEU* 3.5 45.8 - - + -
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Residues in contact with LEU3370 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3357G MET* 6.0 0.7 - - + -
3362G MET* 3.8 31.4 - - + -
3366G GLU 3.0 20.7 + - - +
3367G LEU* 3.7 6.5 - - + +
3369G CYS* 1.3 76.2 - - - +
3371G ARG* 1.3 60.1 + - + +
3373G ILE* 3.2 7.3 + - + +
3374G VAL* 2.9 32.1 + - - +
3400G LEU* 4.3 6.7 - - + -
3418G LEU* 3.6 45.1 - - + +
3419G LEU* 4.1 18.4 - - + -
3421G ARG* 5.3 3.4 - - + -
3422G LEU* 4.3 21.4 - - + +
3425G LEU* 6.4 0.2 - - + -
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Residues in contact with ARG3371 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3239G GLU* 2.9 35.1 + - - -
3279G LEU* 3.5 28.5 - - - +
3282G TRP* 3.3 40.2 - - + +
3308G LEU* 3.0 46.4 + - + +
3309G LEU* 4.4 3.6 - - - +
3311G ALA* 3.9 21.5 - - + -
3312G SER* 4.0 17.0 + - - +
3367G LEU* 3.0 29.1 + - + +
3368G GLY 3.7 1.3 - - - +
3370G LEU* 1.3 73.1 - - + +
3372G ALA* 1.3 61.0 + - - +
3374G VAL* 3.2 4.5 + - - -
3375G LEU* 2.8 26.3 + - - +
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Residues in contact with ALA3372 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3235G ILE* 4.5 5.8 - - + -
3282G TRP* 4.0 8.7 - - - -
3286G ILE* 4.5 22.7 - - + -
3368G GLY 2.9 17.2 + - - +
3369G CYS* 3.2 7.2 + - - +
3371G ARG* 1.3 77.1 - - - +
3373G ILE* 1.3 62.8 + - - +
3375G LEU* 3.3 4.0 + - - +
3376G PHE* 3.0 31.8 + - + -
3396G VAL* 3.8 22.2 - - + -
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Residues in contact with ILE3373 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2420E LEU* 4.1 8.7 - - + -
3369G CYS 2.9 19.2 + - - +
3370G LEU* 3.2 11.6 + - + +
3372G ALA* 1.3 77.1 - - - +
3374G VAL* 1.3 61.2 + - - +
3376G PHE* 3.3 7.1 - - - +
3393G ARG* 2.8 54.5 + - + +
3396G VAL* 3.6 19.1 - - + -
3397G TYR* 3.9 29.4 - - + +
3400G LEU* 4.3 10.5 - - + -
3419G LEU* 3.9 20.6 - - + -
3422G LEU* 4.0 19.5 - - + -
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Residues in contact with VAL3374 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3304G GLY* 4.4 9.5 - - - +
3307G GLU* 4.0 32.8 - - + +
3308G LEU* 3.8 21.5 - - + -
3370G LEU 2.9 20.4 + - - +
3371G ARG* 3.2 9.4 + - - +
3373G ILE* 1.3 79.4 - - - +
3375G LEU* 1.3 64.3 + - - +
3377G ASN* 3.5 16.8 + - - +
3393G ARG* 4.3 4.0 - - - +
3422G LEU* 3.8 24.5 - - + -
3425G LEU* 4.0 15.0 - - + -
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Residues in contact with LEU3375 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3282G TRP* 3.6 24.9 - - + -
3283G ALA* 4.2 6.5 - - + -
3286G ILE* 4.3 19.1 - - + -
3289G PHE* 3.8 39.9 - - + -
3300G LEU* 3.5 32.6 - - + +
3301G LEU* 3.9 25.1 - - + -
3304G GLY* 6.0 0.2 - - - -
3308G LEU* 4.2 13.2 - - + -
3371G ARG 2.8 15.9 + - - +
3372G ALA* 3.5 4.9 - - - +
3374G VAL* 1.3 78.6 - - - +
3376G PHE* 1.3 63.4 + - + +
3377G ASN* 2.9 9.0 + - - +
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Residues in contact with PHE3376 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3230G MET* 3.8 18.2 - - + -
3286G ILE* 3.8 26.0 - - + -
3287G PRO 3.7 18.2 - - - -
3289G PHE* 4.1 26.2 - + + -
3292G LEU* 4.2 4.7 - - + -
3300G LEU* 4.3 10.5 - - + -
3372G ALA* 3.0 22.1 + - + +
3373G ILE 3.5 3.4 - - - +
3375G LEU* 1.3 77.0 - - + +
3377G ASN* 1.3 59.4 + - - +
3378G PRO* 3.2 5.4 - - - +
3389G VAL* 3.5 22.1 - - + +
3392G LEU* 3.6 37.2 - - + -
3393G ARG* 2.9 30.2 + - + +
3396G VAL* 3.8 14.8 - - + -
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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