Contacts of the strand formed by residues 75 - 79 (chain P) in PDB entry 1ZGL
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 SER 75 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22P SER* 3.5 4.9 + - - -
23P CYS 3.0 33.4 + - - +
32P VAL* 4.0 29.7 - - - +
34P TRP* 3.2 21.2 + - - -
49P TYR* 4.5 4.0 - - - -
68P ARG 3.1 16.7 + - - -
69P GLN* 4.2 7.2 - - - -
70P PHE* 4.7 0.4 - - - -
73P SER 3.7 0.2 + - - -
74P ARG* 1.3 77.8 + - - +
76P GLU* 1.3 72.1 + - - +
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Residues in contact with GLU 76 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20P THR* 4.1 17.5 - - + +
21P LEU 3.5 12.4 - - - +
22P SER* 4.4 2.6 + - - +
34P TRP* 4.4 0.6 + - - -
67P GLY* 3.3 3.6 - - - -
68P ARG* 3.1 32.2 + - + +
70P PHE* 3.3 20.6 - - + -
74P ARG* 3.2 41.2 + - - +
75P SER* 1.3 78.2 + - - +
77P MET* 1.3 61.3 + - - +
78P ASN 4.2 0.2 - - - -
68R ARG* 3.2 33.9 + - - -
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Residues in contact with MET 77 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19P VAL 3.8 0.3 - - - +
20P THR* 3.4 2.8 - - - -
21P LEU* 2.8 76.8 + - + -
34P TRP* 3.1 43.2 - - + +
46P LEU* 5.1 3.1 - - - -
47P PHE* 3.7 18.4 - - + -
65P PHE* 6.1 0.9 - - - -
66P SER 3.6 13.5 - - - +
67P GLY* 5.0 0.4 - - - -
76P GLU* 1.3 75.1 - - - +
78P ASN* 1.3 65.1 + - - +
79P VAL* 5.0 10.5 - - + -
90P TYR* 4.1 22.4 - - + -
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Residues in contact with ASN 78 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18P GLN* 2.9 30.1 + - - +
19P VAL 3.4 6.0 + - - +
20P THR* 3.6 16.4 + - + +
64P ARG 4.0 0.3 - - - +
65P PHE* 3.4 2.9 - - - -
66P SER* 2.8 57.8 + - - +
67P GLY* 4.7 0.2 - - - -
76P GLU 4.2 0.6 - - - -
77P MET* 1.3 76.8 - - - +
79P VAL* 1.3 71.6 + - - +
80P SER* 3.2 20.0 + - - -
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Residues in contact with VAL 79 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18P GLN* 3.4 4.9 - - - -
19P VAL* 3.1 38.2 + - + +
21P LEU* 5.4 2.9 - - + -
64P ARG* 3.0 7.2 - - - +
65P PHE* 3.4 40.4 - - + -
77P MET* 5.0 9.9 - - + +
78P ASN* 1.3 80.7 + - - +
80P SER* 1.3 61.4 + - - +
82P LEU* 3.1 26.9 - - + +
86P ASP* 5.6 0.7 - - + +
90P TYR* 4.8 13.0 - - + +
114P LEU* 4.9 5.2 - - + -
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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