Contacts of the helix formed by residues 924 - 932 (chain B) in PDB entry 1ZYC
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 THR 924 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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922B PHE* 4.9 1.7 - - - +
923B SER* 1.3 87.3 + - - +
925B GLY* 1.3 62.4 + - - +
926B MET* 3.9 3.3 + - - +
927B GLU* 2.7 49.5 + - + +
928B ARG* 3.6 3.6 + - - +
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Residues in contact with GLY 925 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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924B THR* 1.3 72.6 - - - +
926B MET* 1.3 63.5 + - - +
927B GLU 2.8 4.9 + - - -
928B ARG* 2.7 37.3 + - - +
929B VAL* 3.4 6.9 + - - +
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Residues in contact with MET 926 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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924B THR* 3.9 3.0 + - - +
925B GLY* 1.3 79.2 - - - +
927B GLU* 1.3 57.9 + - - +
929B VAL* 3.7 22.1 - - + +
930B ASN* 3.1 21.3 + - - -
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Residues in contact with GLU 927 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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922B PHE* 3.3 8.7 - - - -
923B SER* 2.9 38.1 + - - -
924B THR* 2.7 34.8 + - + +
925B GLY 2.8 1.2 + - - -
926B MET* 1.3 76.3 - - - +
928B ARG* 1.3 89.3 + - - +
930B ASN* 2.8 20.3 + - - +
931B ILE* 3.1 31.4 + - + +
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Residues in contact with ARG 928 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797B TYR* 6.1 2.4 - - - -
801B HIS* 4.2 27.5 - - - -
886B GLY* 3.6 20.2 + - - -
889B MET* 3.5 28.9 - - - +
890B TYR* 3.4 17.8 + - - -
917B GLU* 3.0 29.1 + - - -
922B PHE* 3.4 32.3 - - + -
924B THR 4.0 4.0 - - - +
925B GLY* 2.7 18.7 + - - +
927B GLU* 1.3 84.1 + - - +
929B VAL* 1.3 57.3 + - - +
930B ASN 2.7 12.0 + - - -
931B ILE* 3.1 9.4 + - - +
932B LEU* 3.2 25.7 + - + +
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Residues in contact with VAL 929 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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886B GLY* 5.5 2.2 - - - -
889B MET* 3.6 38.1 - - + +
925B GLY 3.8 12.3 - - - +
926B MET* 3.7 23.3 - - + +
927B GLU 3.2 0.4 - - - -
928B ARG* 1.3 79.9 - - - +
930B ASN* 1.3 49.6 + - - +
933B LYS* 2.7 51.7 + - + +
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Residues in contact with ASN 930 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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926B MET 3.1 23.0 + - - -
927B GLU* 2.8 11.3 + - - +
928B ARG 2.7 5.1 + - - -
929B VAL* 1.3 73.5 - - - +
931B ILE* 1.3 58.1 + - - +
932B LEU 2.9 1.1 - - - -
933B LYS* 2.7 33.7 + - - +
934B LYS* 2.6 42.8 + - + +
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Residues in contact with ILE 931 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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916B PHE* 3.8 12.6 - - + -
920B TYR* 4.2 13.7 - - + -
921B PRO 5.1 0.9 - - - +
922B PHE* 3.4 34.5 - - + -
927B GLU* 3.4 30.5 - - + +
928B ARG 3.1 2.7 + - - +
930B ASN* 1.3 76.4 - - + +
932B LEU* 1.3 59.2 + - - +
934B LYS* 3.6 12.8 + - - +
935B LEU* 3.3 18.8 + - - +
941B GLU 4.2 1.7 - - - +
943B PRO* 3.5 41.2 - - + +
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Residues in contact with LEU 932 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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889B MET* 3.3 35.7 - - + -
913B ILE* 4.3 19.7 - - + -
916B PHE* 3.7 30.3 - - + -
917B GLU* 3.8 23.3 - - + +
922B PHE* 3.8 15.5 - - + -
928B ARG* 3.2 28.0 + - + +
930B ASN 2.9 0.2 - - - -
931B ILE* 1.3 74.7 - - - +
933B LYS* 1.3 53.5 + - - +
934B LYS 3.0 1.6 - - - -
935B LEU* 2.7 30.9 + - + +
936B ARG* 2.7 24.1 + - + +
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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