Contacts of the helix formed by residues 3317 - 3331 (chain I) in PDB entry 2ZLE
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 SER3317 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3233I MET* 4.4 9.8 - - - +
3234I ALA 2.7 25.2 + - - -
3236I SER* 2.5 23.1 + - - -
3294I LEU* 3.2 30.9 + - - -
3295I ILE* 2.6 20.6 + - - -
3296I GLY* 4.0 0.9 - - - +
3315I ILE 3.6 0.2 + - - -
3316I PRO* 1.3 70.9 - - - +
3318I ASN* 1.3 54.9 + - - -
3320I VAL* 3.1 11.9 + - - +
3321I LYS* 2.9 29.2 + - - +
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Residues in contact with ASN3318 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3234I ALA 3.5 11.9 + - - -
3235I ASP* 2.5 27.5 + - - +
3236I SER* 2.5 37.2 + - - +
3237I ASP* 3.3 19.2 + - - +
3316I PRO* 5.4 0.7 - - + -
3317I SER* 1.3 73.1 + - - +
3319I MET* 1.3 63.0 + - - +
3321I LYS* 3.5 19.3 + - - +
3322I ASN* 3.2 21.7 + - - +
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Residues in contact with MET3319 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3215I SER* 5.8 0.9 - - - -
3315I ILE* 3.7 21.1 - - + -
3316I PRO* 2.9 21.7 + - + +
3318I ASN* 1.3 76.1 - - - +
3320I VAL* 1.3 61.5 + - - +
3322I ASN* 3.2 19.1 + - + +
3323I LEU* 2.8 53.1 + - + +
3335I ARG* 5.6 2.7 - - - -
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Residues in contact with VAL3320 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3174I ILE* 6.0 0.9 - - + -
3182I VAL* 3.7 31.9 - - + -
3217I ILE* 4.3 12.7 - - + +
3233I MET* 5.2 5.4 - - - -
3294I LEU* 5.1 4.3 - - + -
3297I ILE* 4.2 19.1 - - + +
3315I ILE* 3.8 21.3 - - + +
3316I PRO 2.9 23.1 + - - +
3317I SER* 3.1 10.3 + - - +
3319I MET* 1.3 78.0 - - - +
3321I LYS* 1.3 58.9 + - - +
3323I LEU* 4.2 7.3 - - - +
3324I THR* 2.8 34.9 + - + -
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Residues in contact with LYS3321 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3233I MET* 4.1 42.2 + - + +
3234I ALA 5.9 0.4 - - - -
3317I SER 2.9 12.2 + - - +
3318I ASN* 3.6 22.7 - - - +
3320I VAL* 1.3 75.3 - - - +
3322I ASN* 1.3 59.9 + - - +
3324I THR* 3.1 10.5 - - + +
3325I SER* 3.0 40.3 + - - +
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Residues in contact with ASN3322 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3318I ASN 3.2 12.1 + - - +
3319I MET* 3.2 26.6 + - + +
3321I LYS* 1.3 80.3 - - + +
3323I LEU* 1.3 69.2 + - - +
3324I THR 3.4 0.2 + - - -
3325I SER* 3.6 4.8 + - - -
3326I GLN* 3.4 41.2 + - - +
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Residues in contact with LEU3323 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3212I ASP* 3.3 23.3 - - - +
3215I SER* 3.4 26.7 - - - +
3217I ILE* 4.2 17.9 - - + -
3315I ILE* 4.7 0.9 - - + -
3319I MET* 2.8 48.4 + - + +
3320I VAL* 4.2 3.1 - - - +
3322I ASN* 1.3 78.5 - - - +
3324I THR* 1.3 60.0 + - - +
3326I GLN* 3.4 1.6 + - - +
3327I MET* 3.0 34.3 + - + +
3333I VAL* 3.4 23.4 - - + +
3335I ARG* 3.5 17.9 - - - +
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Residues in contact with THR3324 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3174I ILE* 4.8 17.1 - - + +
3182I VAL* 4.4 12.1 - - - +
3217I ILE* 5.3 3.2 - - - +
3219I LEU* 3.3 30.4 - - + +
3233I MET* 5.7 2.9 - - + -
3320I VAL* 2.8 21.6 + - + +
3321I LYS* 3.1 18.2 - - + +
3323I LEU* 1.3 76.5 - - - +
3325I SER* 1.3 70.6 + - - +
3327I MET* 3.2 20.3 + - - +
3328I VAL* 3.2 16.2 + - + +
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Residues in contact with SER3325 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3321I LYS* 3.0 22.0 + - - +
3322I ASN* 4.0 6.0 - - - -
3323I LEU 3.4 0.2 - - - -
3324I THR* 1.3 79.2 - - - +
3326I GLN* 1.3 66.8 + - - +
3328I VAL* 3.1 9.0 + - - +
3329I GLU* 2.9 45.8 + - - +
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Residues in contact with GLN3326 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3322I ASN* 3.4 35.5 + - - +
3323I LEU* 3.4 11.0 + - - +
3324I THR 3.2 0.8 - - - -
3325I SER* 1.3 79.0 - - - +
3327I MET* 1.3 63.9 + - - +
3329I GLU* 5.3 0.2 - - - -
3330I TYR* 3.0 44.1 + - + +
3332I GLN 3.4 11.0 - - - +
3333I VAL* 2.9 18.9 - - + +
3334I LYS* 2.6 42.9 + - - +
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Residues in contact with MET3327 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3209I VAL* 4.1 4.1 - - + +
3210I GLY* 3.3 37.2 - - - +
3211I LYS 3.3 31.4 - - - +
3212I ASP* 3.5 13.9 - - + +
3217I ILE* 3.4 22.7 - - + +
3218I ALA 4.3 0.9 - - - -
3219I LEU* 3.7 22.9 - - + -
3323I LEU* 3.0 21.8 - - + +
3324I THR* 3.2 11.4 + - - +
3326I GLN* 1.3 75.3 - - - +
3328I VAL* 1.3 59.5 + - - +
3331I GLY* 2.9 26.9 + - - -
3332I GLN* 4.1 12.8 + - - +
3333I VAL* 4.3 10.3 - - + +
3490I ARG* 3.8 6.8 + - - -
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Residues in contact with VAL3328 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3178I LYS* 5.7 2.9 - - - +
3180I TYR* 3.8 42.2 - - + +
3209I VAL* 4.6 6.1 - - + -
3219I LEU* 3.9 15.0 - - + -
3324I THR* 3.2 11.5 + - + +
3325I SER* 3.1 12.2 + - - +
3327I MET* 1.3 82.7 - - - +
3329I GLU* 1.3 70.9 + - + +
3330I TYR 3.3 4.0 + - - -
3487I ALA* 3.3 14.4 - - - +
3490I ARG* 4.7 2.6 + - - -
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Residues in contact with GLU3329 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3325I SER* 2.9 35.0 + - - +
3326I GLN 4.7 0.2 - - - +
3328I VAL* 1.3 80.2 - - + +
3330I TYR* 1.3 90.1 + - + +
3485I ASN* 4.1 4.9 + - - -
3487I ALA* 3.5 10.1 - - - +
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Residues in contact with TYR3330 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3326I GLN* 3.0 41.5 + - + +
3328I VAL 3.3 1.8 + - - -
3329I GLU* 1.3 103.1 + - + +
3331I GLY* 1.3 60.6 + - - +
3332I GLN 3.3 11.2 - - - +
3334I LYS* 4.1 31.9 - - + -
3446I ASN* 3.1 22.3 + - - +
3450I ASP* 5.2 8.1 - - - -
3485I ASN* 3.8 19.1 - - + +
3486I ILE* 3.5 7.8 + - - +
3487I ALA* 3.3 19.5 + - - +
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Residues in contact with GLY3331 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3209I VAL 3.9 9.9 - - - +
3210I GLY* 4.7 3.3 - - - -
3327I MET* 2.9 20.4 + - - -
3330I TYR* 1.3 78.5 - - - +
3332I GLN* 1.3 58.5 + - - +
3433I ASN* 2.7 25.6 - - - +
3446I ASN* 4.6 0.7 - - - -
3486I ILE* 3.9 11.7 - - - -
3487I ALA* 4.0 2.3 - - - +
3490I ARG* 3.4 16.6 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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