Contacts of the helix formed by residues 2951 - 2956 (chain H) 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 SER2951 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2947H THR* 3.7 20.6 + - - -
2948H GLU* 3.0 18.5 + - - +
2950H ASN* 1.3 87.1 - - - +
2952H GLU* 1.3 65.6 + - - +
2953H LEU* 4.1 6.5 + - - +
2954H ALA* 3.0 23.9 + - - +
2955H LYS* 3.4 7.8 + - - +
2966H PHE* 3.8 6.2 - - - -
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Residues in contact with GLU2952 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1513D GLN* 4.5 5.2 + - - +
1516D ARG* 2.7 53.3 + - - +
2950H ASN 3.6 1.1 + - - -
2951H SER* 1.3 71.5 - - - +
2953H LEU* 1.3 50.6 + - + +
2955H LYS* 3.8 7.9 - - - +
2956H ALA 2.6 27.4 + - - -
4144K ALA* 2.2 32.3 - - + +
4145K MET* 2.7 0.7 - - - +
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Residues in contact with LEU2953 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1513D GLN* 6.2 1.1 - - - +
2951H SER* 3.1 6.7 - - - +
2952H GLU* 1.3 68.9 - - + +
2954H ALA* 1.3 56.9 + - - +
2957H MET* 3.0 12.6 - - + +
2966H PHE* 3.5 7.4 - - + -
2968H SER* 3.9 16.4 - - - +
4143K LYS 2.4 18.6 - - - +
4144K ALA* 3.0 5.5 + - - +
4145K MET* 1.4 59.2 - - - +
4146K LYS* 1.2 236.0 - - + +
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Residues in contact with ALA2954 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2949H LEU* 3.6 28.5 - - - +
2951H SER* 3.0 23.0 + - - +
2953H LEU* 1.3 78.8 - - - +
2955H LYS* 1.3 58.7 + - - +
2958H LYS* 3.3 2.9 + - - -
2959H VAL* 3.1 47.1 + - + +
2962H GLN* 4.8 1.6 + - - +
2966H PHE* 3.6 20.4 - - + -
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Residues in contact with LYS2955 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2949H LEU 5.1 3.6 - - - +
2950H ASN* 3.6 26.9 + - - +
2951H SER 3.4 8.2 + - - +
2952H GLU* 3.8 8.7 - - - +
2954H ALA* 1.3 80.3 - - + +
2956H ALA 1.3 27.0 - - - +
2957H MET 2.9 2.7 - - - -
2958H LYS* 2.8 20.0 + - - +
2962H GLN* 5.7 2.9 - - - +
4145K MET* 1.0 125.9 - - - +
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Residues in contact with ALA2956 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2952H GLU 2.6 4.2 + - - +
2955H LYS* 1.3 49.5 - - - +
2957H MET* 1.3 47.7 + - - -
4141K LEU* 1.4 41.6 - - + +
4142K ALA* 3.1 2.3 - - - -
4144K ALA* 2.2 20.4 - - + +
4145K MET* 0.7 212.3 - - + +
4154K PHE* 2.7 10.4 - - - -
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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