Contacts of the strand formed by residues 2784 - 2788 (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 TYR2784 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2777H ILE* 3.5 2.4 - - - -
2778H ILE* 2.6 43.2 + - + -
2779H ASP* 3.1 35.7 + - + +
2782H LYS* 3.4 38.0 + - + +
2783H GLY* 1.3 75.9 - - - +
2785H VAL* 1.3 56.3 + - - +
2786H VAL 4.2 0.2 - - - -
2813H VAL* 4.6 9.4 - - + +
2823H LEU* 4.2 16.8 - - + -
2824H ILE 3.4 6.5 - - - +
2825H GLN* 3.4 37.5 + - + -
2932H VAL* 3.8 38.0 - - + +
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Residues in contact with VAL2785 (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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2739H VAL* 4.1 13.9 - - + -
2741H ILE* 4.5 1.3 - - + -
2775H GLY* 3.7 10.5 - - - -
2776H VAL 3.2 23.3 - - - +
2777H ILE* 3.9 17.5 - - + -
2784H TYR* 1.3 76.0 - - - +
2786H VAL* 1.3 68.4 + - - +
2787H THR* 3.9 0.5 + - - +
2800H VAL* 5.2 0.4 - - + -
2823H LEU* 3.0 6.2 - - - +
2824H ILE* 2.8 58.8 + - + +
2826H ILE* 3.9 33.2 - - + -
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Residues in contact with VAL2786 (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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2775H GLY* 3.0 5.7 - - - -
2776H VAL* 2.8 60.4 + - + +
2778H ILE* 4.3 18.3 - - + +
2784H TYR 4.2 0.4 + - - -
2785H VAL* 1.3 71.3 - - - +
2787H THR* 1.3 66.4 + - - +
2821H ILE* 4.2 13.2 - - + -
2822H ALA 3.5 10.3 - - - +
2823H LEU* 3.8 6.6 - - + +
2901H ILE* 3.9 24.9 - - + +
2924H VAL* 3.7 26.0 - - + -
2928H THR* 4.4 10.1 - - - +
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Residues in contact with THR2787 (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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2741H ILE* 3.6 24.4 - - + +
2774H SER 2.6 26.3 + - - -
2785H VAL 4.5 2.5 - - - +
2786H VAL* 1.3 80.4 - - - +
2788H ASN* 1.3 67.4 + - - +
2791H VAL* 4.3 6.9 - - - +
2792H VAL* 3.9 23.1 - - + -
2821H ILE* 3.5 6.4 - - - +
2822H ALA* 2.6 46.9 + - + +
2824H ILE* 4.4 11.7 - - + -
2901H ILE* 5.0 7.6 - - - -
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Residues in contact with ASN2788 (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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2774H SER 4.4 5.2 + - - +
2787H THR* 1.3 92.9 + - - +
2789H ASN* 1.3 64.6 + - - +
2790H HIS* 3.3 30.7 - - + +
2791H VAL* 3.1 24.9 + - + +
2792H VAL* 3.6 5.0 + - - +
2820H ASP* 3.2 22.9 + - - +
2822H ALA* 4.2 1.3 - - - -
2887H SER 4.0 0.5 - - - +
2888H GLY 3.1 18.1 - - - +
2889H GLY* 4.5 2.6 - - - -
2901H ILE* 3.9 7.4 - - - +
2902H ASN 2.7 25.9 + - - -
2903H THR* 3.7 4.8 - - - +
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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