Contacts of the strand formed by residues 2795 - 2801 (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 ALA2795 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2743H VAL* 3.3 24.9 - - + -
2744H GLU 3.7 5.2 - - - +
2745H GLY* 4.3 0.2 - - - -
2792H VAL* 2.9 20.9 + - + +
2793H ASP 3.1 0.6 - - - -
2794H ASN* 1.3 80.8 - - - +
2796H THR* 1.3 59.5 + - - +
2798H ILE* 4.0 23.3 - - + -
2812H MET* 5.5 6.2 - - + +
3039H VAL* 5.7 5.4 - - - +
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Residues in contact with THR2796 (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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2744H GLU* 2.8 10.7 + - - +
2745H GLY* 3.4 15.2 - - - -
2746H SER* 3.7 10.9 + - - -
2794H ASN 3.6 1.1 + - - -
2795H ALA* 1.3 75.0 - - - +
2797H VAL* 1.3 72.9 + - + +
2798H ILE* 4.3 1.5 - - - +
3039H VAL* 6.5 1.3 - - - -
3045H PHE* 5.0 19.4 - - + -
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Residues in contact with VAL2797 (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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2742H ASN 3.8 0.9 - - - +
2743H VAL* 3.4 2.4 - - - +
2744H GLU* 2.8 64.1 + - + +
2795H ALA* 4.7 0.2 - - - -
2796H THR* 1.3 92.2 - - + +
2798H ILE* 1.3 64.6 + - - +
2799H LYS* 4.1 30.5 - - + -
2809H ASP* 5.6 0.9 - - - +
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Residues in contact with ILE2798 (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 20.6 - - + -
2742H ASN 3.6 2.2 - - - -
2743H VAL* 4.3 9.9 - - + +
2792H VAL* 5.1 6.5 - - + -
2795H ALA* 4.0 18.6 - - + -
2796H THR 5.4 1.1 - - - +
2797H VAL* 1.3 77.5 - - - +
2799H LYS* 1.3 76.9 + - - +
2800H VAL* 3.7 5.8 - - + -
2809H ASP* 3.8 2.4 - - - +
2810H ALA* 2.9 50.5 + - + +
2811H LYS* 4.9 5.4 - - - -
2812H MET* 5.0 11.4 - - + +
2824H ILE* 3.6 27.6 - - + -
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Residues in contact with LYS2799 (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* 3.3 4.5 - - - -
2742H ASN* 2.7 51.8 + - + +
2744H GLU* 5.9 1.1 + - - -
2797H VAL* 4.1 21.5 - - + -
2798H ILE* 1.3 80.8 - - - +
2800H VAL* 1.3 63.1 + - - +
2807H LYS* 5.3 19.9 - - - +
2808H PHE 3.8 5.6 - - - +
2809H ASP* 3.8 23.8 - - - +
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Residues in contact with VAL2800 (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* 3.5 33.4 - - + -
2740H SER 3.4 5.8 - - - +
2741H ILE* 4.2 3.8 - - + -
2785H VAL* 5.5 0.7 - - + -
2798H ILE* 3.7 17.7 - - + -
2799H LYS* 1.3 81.3 - - - +
2801H GLN* 1.3 66.9 + - - +
2802H LEU* 4.6 3.4 - - + +
2806H ARG 4.1 0.5 - - - +
2807H LYS* 3.5 4.0 - - - +
2808H PHE* 2.8 45.0 + - + +
2810H ALA* 3.9 9.4 - - + -
2824H ILE* 3.8 16.4 - - + -
2826H ILE* 4.5 22.4 - - + -
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Residues in contact with GLN2801 (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* 3.7 0.5 - - - -
2740H SER* 3.1 45.4 + - - +
2800H VAL* 1.3 77.2 - - - +
2802H LEU* 1.3 73.8 + - - +
2805H GLY* 3.3 21.8 - - - +
2806H ARG 3.4 10.3 - - - +
2807H LYS* 3.9 26.3 - - + +
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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