Contacts of the strand formed by residues 118 - 123 (chain P) in PDB entry 1ZD2
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 118 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4P ARG* 3.0 33.6 + - - +
5P ALA* 3.2 11.8 - - - +
6P ALA 3.1 22.0 + - - +
116P GLY 4.3 4.3 + - - -
117P PHE* 1.3 72.0 - - - +
119P THR* 1.3 60.0 + - - +
148P ASP* 3.1 25.6 - - + +
149P PHE* 4.5 15.7 - - + -
173P LEU* 5.0 16.4 - - + +
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Residues in contact with THR 119 (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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6P ALA* 3.2 16.8 - - + +
8P PHE* 5.1 0.2 - - - -
109P ALA* 3.7 27.6 - - + +
112P LEU* 4.7 0.2 - - + -
113P ARG* 3.8 23.0 - - + +
117P PHE* 4.3 4.5 - - + +
118P THR* 1.3 76.9 - - - +
120P ALA* 1.3 67.1 + - - +
146P HIS 3.5 5.1 + - - +
147P PHE* 3.2 36.4 - - + -
148P ASP* 2.8 35.9 + - - +
149P PHE* 3.3 2.4 + - - -
173P LEU* 6.1 0.2 - - - -
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Residues in contact with ALA 120 (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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6P ALA 3.1 5.1 + - - +
7P VAL* 3.1 15.8 - - + +
8P PHE* 2.7 33.1 + - - -
119P THR* 1.3 80.1 - - - +
121P ILE* 1.3 59.2 + - - +
122P LEU 4.0 0.4 - - - -
147P PHE* 3.8 3.5 - - - -
149P PHE* 3.1 28.5 - - + +
151P ILE* 5.5 1.8 - - + -
169P LEU* 4.7 3.4 - - + -
173P LEU* 4.2 21.8 - - + -
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Residues in contact with ILE 121 (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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7P VAL* 4.5 0.2 - - - -
8P PHE 3.0 12.6 - - - +
10P LEU* 4.3 19.3 - - + +
14P LEU* 3.7 21.8 - - + -
120P ALA* 1.3 72.7 - - - +
122P LEU* 1.3 56.5 + - - +
123P THR* 4.0 13.7 - - + -
140P MET* 5.0 3.4 - - + -
143P LEU* 4.2 22.2 - - + -
144P LYS* 4.9 1.3 - - - +
147P PHE* 3.7 38.6 - - + -
149P PHE 3.0 7.0 + - - +
150P LEU* 3.4 29.1 - - + +
151P ILE* 2.7 34.2 + - - +
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Residues in contact with LEU 122 (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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7P VAL* 3.6 19.7 - - + +
8P PHE 2.8 7.9 + - - -
9P ASP* 3.4 24.9 - - - +
121P ILE* 1.3 71.6 - - - +
123P THR* 1.3 61.2 + - - +
151P ILE* 3.5 39.5 - - + +
160P LYS* 3.8 26.2 - - + -
165P ILE* 3.7 24.9 - - + -
166P TYR* 4.7 7.9 - - + -
169P LEU* 3.9 21.5 - - + -
182P PHE* 3.4 25.6 - - + -
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Residues in contact with THR 123 (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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10P LEU* 3.8 23.5 - - + +
121P ILE* 4.0 15.9 - - + -
122P LEU* 1.3 78.0 - - - +
124P ASN* 1.3 64.6 + - - +
125P THR* 3.3 11.0 + - + -
140P MET* 5.3 0.7 - - + -
150P LEU* 4.4 4.9 - - + -
151P ILE 3.1 12.2 + - - +
152P GLU* 4.2 17.5 - - + -
153P SER* 2.8 33.1 + - - -
160P LYS* 4.1 1.8 - - - +
165P ILE* 5.4 0.5 - - - +
900P PO4 2.5 28.2 + - - -
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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