Contacts of the strand formed by residues 2916 - 2920 (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 GLY2916 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2876H ILE 3.3 0.5 - - - +
2877H GLN* 3.1 8.8 - - - +
2878H THR* 2.8 53.9 + - - +
2881H ALA* 3.9 12.5 - - - +
2902H ASN* 4.9 5.2 - - - -
2912H ASN* 5.5 1.8 - - - -
2915H ILE* 1.3 71.0 - - - +
2917H PHE* 1.3 65.7 + - - -
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Residues in contact with PHE2917 (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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2875H PHE* 4.1 24.2 - + + -
2876H ILE 3.2 3.6 - - - -
2877H GLN* 4.1 18.4 - - + -
2902H ASN* 3.7 3.8 - - - +
2903H THR* 2.7 48.8 + - + +
2905H ILE* 3.6 44.9 - - + -
2913H ILE* 3.7 11.4 - - + -
2915H ILE* 3.4 30.3 - - + -
2916H GLY* 1.3 75.9 - - - -
2918H ALA* 1.3 61.4 + - - +
3648J PHE* 5.8 0.2 - + - -
3650J LEU* 3.9 28.9 - - + -
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Residues in contact with ALA2918 (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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2875H PHE* 3.5 8.6 - - - -
2876H ILE* 2.7 52.4 + - + +
2878H THR* 5.7 0.9 - - + -
2891H LEU* 4.3 9.2 - - + -
2900H GLY* 4.3 5.2 - - - -
2901H ILE 3.3 21.1 - - - +
2902H ASN* 3.8 14.1 - - - +
2916H GLY 4.2 0.2 - - - -
2917H PHE* 1.3 75.6 - - - +
2919H ILE* 1.3 68.6 + - - +
2920H PRO 3.5 0.3 - - - -
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Residues in contact with ILE2919 (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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2819H SER* 3.2 37.5 - - - +
2821H ILE* 3.7 26.2 - - + -
2875H PHE* 3.6 28.7 - - + -
2900H GLY* 2.8 23.6 - - - -
2901H ILE 2.9 16.4 + - - +
2903H THR* 4.7 5.6 - - + -
2918H ALA* 1.3 72.5 - - - +
2920H PRO* 1.3 74.6 - - + +
2923H MET* 3.7 28.7 - - + -
2924H VAL* 3.8 7.9 - - + +
2927H LEU* 4.7 2.0 - - + -
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Residues in contact with PRO2920 (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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2840H SER* 3.4 20.4 - - - +
2874H ASN* 3.1 47.1 - - + +
2875H PHE* 4.5 0.9 - - - -
2876H ILE* 4.2 10.5 - - + -
2899H ILE 3.5 5.2 - - - +
2918H ALA 3.6 2.7 - - - +
2919H ILE* 1.3 90.8 - - + +
2921H SER* 1.3 68.2 + - - +
2922H ASN* 4.5 0.4 - - + +
2923H MET* 2.9 28.7 + - + +
2924H VAL* 2.9 12.2 + - - +
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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