Contacts of the strand formed by residues 918 - 923 (chain C) 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 TYR 918 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398B MET* 4.7 5.0 - - + +
399B PRO* 3.3 44.3 + - + +
400B SER* 4.0 7.0 - - - -
401B LEU* 3.7 27.6 - - + +
538B SER* 5.2 3.8 - - - -
916C GLY 3.6 0.2 + - - -
917C ASP* 1.3 77.0 - - - +
919C THR* 1.3 62.1 + - - +
935C GLY 3.4 14.4 - - - +
936C ILE* 3.4 18.6 - - + -
937C VAL* 5.1 0.3 - - - +
963C ASN* 4.0 19.8 - - - +
964C LEU* 3.6 37.9 + - + -
969C ILE* 4.8 1.7 - - - +
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Residues in contact with THR 919 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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918C TYR* 1.3 75.4 + - - +
920C VAL* 1.3 64.1 + - - +
934C SER* 3.5 3.6 - - - -
935C GLY 2.8 33.9 + - - +
936C ILE* 3.9 11.4 - - - +
937C VAL* 3.8 11.3 - - - +
948C THR* 3.0 28.2 + - - +
950C ALA* 3.5 13.9 - - + -
961C LEU* 3.4 20.8 - - + +
962C VAL 3.8 3.4 - - - -
964C LEU* 5.6 3.4 - - - +
969C ILE* 3.5 23.4 - - - +
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Residues in contact with VAL 920 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797C LEU* 4.9 7.6 - - + -
800C MET* 3.2 18.6 - - + -
801C LEU* 4.3 12.3 - - + -
919C THR* 1.3 76.6 - - - +
921C ALA* 1.3 64.1 + - - +
922C ILE* 4.7 3.4 - - + +
932C VAL* 3.7 23.3 - - + -
933C THR 3.5 14.4 - - - +
934C SER* 4.7 6.5 - - - -
960C ALA 3.8 0.5 - - - +
961C LEU* 3.5 4.2 - - - +
962C VAL* 2.8 75.8 + - + +
963C ASN 4.1 2.0 - - - +
964C LEU* 5.5 2.7 - - + -
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Residues in contact with ALA 921 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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920C VAL* 1.3 71.4 - - - +
922C ILE* 1.3 66.3 + - - +
923C GLY 4.3 0.4 - - - -
931C THR 3.9 0.2 - - - +
932C VAL* 3.2 4.9 - - - +
933C THR* 2.8 43.0 + - + +
950C ALA* 3.6 25.2 - - + +
951C ALA* 5.7 0.2 - - - -
960C ALA 3.2 9.0 - - - +
961C LEU* 4.1 6.0 - - + +
972C ASN* 3.9 13.7 - - - +
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Residues in contact with ILE 922 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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801C LEU* 4.5 12.3 - - + -
804C VAL* 3.7 30.1 - - + -
805C MET* 4.0 28.3 - - + -
808C VAL* 4.0 28.6 - - + +
844C SER* 4.6 3.4 - - - -
920C VAL* 4.7 6.7 - - + +
921C ALA* 1.3 82.7 - - - +
923C GLY* 1.3 62.2 + - - +
930C GLU* 5.1 3.8 - - + +
931C THR 3.5 9.6 - - - +
932C VAL* 4.3 11.2 - - + -
958C GLY* 5.4 0.2 - - - -
959C GLY* 3.5 4.6 + - - -
960C ALA* 2.9 37.0 + - + +
962C VAL* 5.0 8.7 - - + -
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Residues in contact with GLY 923 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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844C SER* 3.5 14.4 - - - -
921C ALA 4.3 0.2 - - - -
922C ILE* 1.3 77.1 - - - +
924C ASN* 1.3 59.3 + - - -
925C PRO* 3.1 9.4 - - - +
930C GLU* 3.4 5.4 - - - -
931C THR 2.8 33.7 + - - -
958C GLY* 4.2 15.0 - - - -
959C GLY 4.2 0.2 - - - -
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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