Contacts of the strand formed by residues 2848 - 2853 (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 TYR2848 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2846H GLY 3.6 0.4 + - - -
2847H ASP* 1.3 77.1 - - - +
2849H THR* 1.3 63.2 + - - +
2865H GLY* 3.4 14.8 - - - +
2866H ILE* 3.4 18.8 - - + -
2867H VAL* 5.1 0.2 - - - +
2893H ASN* 4.0 19.8 - - - +
2894H LEU* 3.6 37.2 + - + -
2899H ILE* 4.8 1.7 - - - +
3516J MET* 4.7 5.1 - - + +
3517J PRO* 3.3 43.4 + - + +
3518J SER* 4.0 7.6 - - - -
3519J LEU* 3.7 27.5 - - + +
3656J SER* 5.2 4.0 - - - -
3686J LEU* 5.9 0.2 - - - +
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Residues in contact with THR2849 (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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2848H TYR* 1.3 75.3 + - - +
2850H VAL* 1.3 64.2 + - - +
2864H SER* 3.5 3.3 - - - -
2865H GLY 2.8 33.5 + - - +
2866H ILE* 3.9 12.3 - - - +
2867H VAL* 3.8 11.3 - - - +
2878H THR* 3.0 27.4 + - - +
2880H ALA* 3.5 13.5 - - + -
2891H LEU* 3.4 20.5 - - + +
2892H VAL 3.8 3.1 - - - -
2893H ASN* 5.1 0.2 - - - +
2894H LEU* 5.6 3.2 - - - +
2899H ILE* 3.5 23.4 - - - +
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Residues in contact with VAL2850 (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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2727H LEU* 4.9 7.2 - - + -
2730H MET* 3.2 18.4 - - + -
2731H LEU* 4.3 12.8 - - + -
2849H THR* 1.3 76.8 - - - +
2851H ALA* 1.3 64.5 + - - +
2852H ILE* 4.7 3.8 - - + +
2862H VAL* 3.7 23.3 - - + -
2863H THR 3.5 13.0 - - - +
2864H SER* 4.7 6.1 - - - -
2890H ALA 3.8 0.5 - - - +
2891H LEU* 3.5 3.4 - - - +
2892H VAL* 2.8 74.4 + - + +
2893H ASN 4.1 2.0 - - - +
2894H LEU* 5.5 3.6 - - + -
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Residues in contact with ALA2851 (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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2850H VAL* 1.3 71.8 - - - +
2852H ILE* 1.3 66.1 + - - +
2861H THR 3.9 0.3 - - - +
2862H VAL* 3.2 5.2 - - - +
2863H THR* 2.8 43.3 + - + +
2880H ALA* 3.6 24.6 - - + +
2890H ALA 3.2 8.7 - - - +
2891H LEU* 4.1 5.8 - - + +
2902H ASN* 3.9 13.5 - - - +
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Residues in contact with ILE2852 (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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2731H LEU* 4.5 12.1 - - + -
2734H VAL* 3.7 29.4 - - + -
2735H MET* 4.0 27.4 - - + -
2738H VAL* 4.0 29.6 - - + +
2774H SER* 4.6 2.8 - - - -
2850H VAL* 4.7 6.5 - - + +
2851H ALA* 1.3 82.3 - - - +
2853H GLY* 1.3 61.7 + - - +
2860H GLU* 5.1 4.7 - - + +
2861H THR 3.5 9.2 - - - +
2862H VAL* 4.3 11.7 - - + -
2889H GLY* 3.5 4.8 + - - -
2890H ALA* 2.9 37.5 + - + +
2892H VAL* 5.0 9.0 - - + -
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Residues in contact with GLY2853 (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* 3.5 14.1 - - - -
2851H ALA 4.3 0.4 - - - -
2852H ILE* 1.3 76.8 - - - +
2854H ASN* 1.3 59.0 + - - -
2855H PRO* 3.1 8.7 - - - +
2860H GLU* 3.4 5.4 - - - -
2861H THR 2.8 33.3 + - - -
2888H GLY* 4.2 15.3 - - - -
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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