Contacts of the strand formed by residues 4801 - 4807 (chain M) 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 ILE4801 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4766M VAL* 4.2 16.2 - - + -
4767M THR 3.5 2.5 - - - +
4769M ASN* 4.0 1.5 - - - +
4796M ASP 3.0 26.1 + - - +
4799M SER* 3.3 28.8 + - - +
4800M ASP* 1.3 78.3 - - - +
4802M ALA* 1.3 65.4 + - - +
4881M ILE* 3.8 31.9 - - + -
4899M ILE* 3.7 27.4 - - + -
4904M VAL* 4.3 17.0 - - + +
4907M LEU* 4.2 15.9 - - + -
4908M THR* 5.3 3.6 - - - +
4911M MET* 3.4 12.4 - - + +
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Residues in contact with ALA4802 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4766M VAL* 3.5 6.5 - - - +
4767M THR* 2.6 48.2 + - + +
4768M ASN 4.2 1.1 - - - +
4769M ASN* 3.9 8.7 - - - -
4772M VAL* 3.7 28.3 - - + -
4794M GLY 3.5 13.5 - - - +
4795M LYS* 3.9 8.7 - - + +
4801M ILE* 1.3 77.0 - - - +
4803M LEU* 1.3 60.6 + - - +
4908M THR* 5.6 0.2 - - - -
4911M MET* 4.3 3.1 - - - -
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Residues in contact with LEU4803 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4758M ILE* 5.1 4.5 - - + -
4764M TYR* 4.2 16.4 - - + -
4765M VAL 3.0 36.8 - - - +
4766M VAL* 3.8 7.0 - - + +
4792M MET* 4.0 0.5 - - - +
4793M VAL* 3.1 36.6 + - + +
4794M GLY 2.8 14.0 + - - +
4802M ALA* 1.3 71.5 - - - +
4804M ILE* 1.3 73.5 + - - +
4908M THR* 3.3 30.3 - - + +
4911M MET* 3.7 17.3 - - + -
4912M VAL* 3.9 27.8 - - + -
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Residues in contact with ILE4804 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4721M ILE* 3.9 17.5 - - + -
4764M TYR* 3.4 6.8 - - - -
4765M VAL* 2.8 52.9 + - + +
4767M THR* 4.4 6.1 - - + -
4772M VAL* 4.3 20.9 - - + -
4778M ILE* 3.6 32.8 - - + -
4780M VAL* 3.8 12.3 - - + -
4790M ALA* 3.8 9.9 - - + -
4791M LYS 3.4 14.8 - - - +
4792M MET* 4.4 12.3 - - - -
4793M VAL* 3.4 4.5 - - - -
4803M LEU* 1.3 83.5 - - - +
4805M GLN* 1.3 63.4 + - - +
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Residues in contact with GLN4805 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4762M LYS* 2.9 39.7 - - - +
4763M GLY 3.1 1.3 - - - +
4764M TYR* 3.4 33.5 + - + -
4790M ALA* 3.2 4.3 - - - -
4791M LYS* 3.0 34.7 + - + +
4793M VAL* 4.5 7.0 - - + +
4804M ILE* 1.3 74.8 - - - +
4806M ILE* 1.3 69.6 + - - +
4807M GLN* 3.2 14.2 + - - +
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Residues in contact with ILE4806 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4757M ILE* 4.6 5.2 - - + -
4762M LYS 4.4 1.6 - - - +
4763M GLY* 2.7 20.8 + - - +
4765M VAL* 3.9 25.8 - - + -
4780M VAL* 4.5 22.4 - - + -
4782M LEU* 4.6 7.4 - - + -
4788M PHE* 3.4 43.5 - - + -
4789M ASP 3.4 4.9 - - - -
4790M ALA* 4.3 1.8 - - + -
4804M ILE* 5.9 0.2 - - + -
4805M GLN* 1.3 79.0 - - - +
4807M GLN* 1.3 65.7 + - - +
4808M ASN 3.4 3.1 + - - -
4809M PRO* 3.6 18.2 - - + +
4812M LEU* 3.6 29.6 - - + -
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Residues in contact with GLN4807 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4788M PHE* 3.9 6.6 - - - -
4789M ASP* 2.5 40.8 + - + +
4791M LYS* 3.2 47.6 - - + +
4805M GLN* 3.3 26.2 + - - +
4806M ILE* 1.3 79.1 - - - +
4808M ASN* 1.3 80.9 + - - +
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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