Contacts of the strand formed by residues 136 - 146 (chain F) in PDB entry 1ZMC
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 136 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128F THR* 4.2 14.1 - - + -
129F ALA 3.2 5.6 - - - +
130F THR* 3.6 21.5 - - + +
131F LYS* 4.7 4.9 - - - +
134F GLY 3.6 9.2 + - - +
135F GLY* 1.3 80.4 - - - +
137F GLN* 1.3 64.7 + - - +
138F VAL* 4.2 5.0 - - - +
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Residues in contact with GLN 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F PRO* 3.5 22.4 - - - +
5F ILE* 3.6 22.6 - - + +
115F VAL* 4.3 19.5 - - + -
127F VAL 4.0 0.7 - - - +
128F THR* 3.6 1.3 - - - -
129F ALA* 2.9 40.9 + - + +
131F LYS* 5.7 6.1 - - + -
136F THR* 1.3 76.7 - - - +
138F VAL* 1.3 89.0 + - - +
139F ILE* 4.0 10.3 + - + +
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Residues in contact with VAL 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F PRO* 3.4 12.1 - - + +
5F ILE 2.9 24.2 + - - -
126F GLN* 3.4 37.5 - - + +
127F VAL 3.7 3.1 - - - +
128F THR* 3.9 20.9 - - + +
136F THR* 4.2 4.5 - - - +
137F GLN* 1.3 87.2 + - - +
139F ILE* 1.3 64.1 + - - +
140F ASP* 3.9 13.0 - - - +
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Residues in contact with ILE 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F ILE* 3.2 33.7 - - + +
7F ALA* 4.3 3.8 - - + -
10F THR* 3.5 27.1 - - + +
33F VAL* 4.1 18.6 - - + -
35F ILE* 3.4 37.7 - - + -
115F VAL* 4.5 9.0 - - + -
126F GLN* 3.5 3.1 - - - +
127F VAL* 2.9 39.6 + - + +
129F ALA* 4.8 1.1 - - + -
137F GLN* 4.3 11.2 - - + +
138F VAL* 1.3 78.8 - - - +
140F ASP* 1.3 69.5 + - - +
141F THR* 3.7 3.1 + - - +
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Residues in contact with ASP 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F PRO* 4.7 9.2 - - - +
5F ILE 2.8 14.4 + - - +
6F ASP* 3.0 14.8 - - + +
7F ALA 2.8 23.6 + - - +
125F ASN 3.4 6.6 - - - +
126F GLN* 3.2 30.2 + - - +
138F VAL* 3.9 10.4 - - - +
139F ILE* 1.3 71.6 - - - +
141F THR* 1.3 59.6 + - - +
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Residues in contact with THR 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F ALA* 3.0 14.4 + - - -
8F ASP 3.3 8.1 + - - -
10F THR* 2.9 30.0 + - - +
125F ASN* 2.8 36.0 + - - +
127F VAL* 4.4 4.3 - - + -
139F ILE* 4.0 9.0 - - - +
140F ASP* 1.3 77.0 - - - +
142F LYS* 1.3 66.4 + - - +
143F ASN 2.9 25.4 + - - +
144F ILE* 3.9 15.0 - - + -
314F ASN* 4.9 0.2 + - - -
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Residues in contact with LYS 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F ALA 3.1 9.4 + - - +
8F ASP* 2.6 40.1 + - + +
125F ASN* 3.3 8.7 - - - +
141F THR* 1.3 71.8 - - - +
143F ASN* 1.3 74.1 + - - +
314F ASN* 3.0 23.4 + - - +
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Residues in contact with ASN 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414B ARG* 5.4 6.1 + - - -
8F ASP* 2.6 30.4 + - - +
9F VAL* 4.3 2.1 - - + +
10F THR 3.1 12.9 + - - -
30F PHE* 5.2 5.5 - - - -
141F THR* 2.9 19.8 + - - +
142F LYS* 1.3 91.3 - - - +
144F ILE* 1.3 64.8 + - - +
314F ASN* 3.4 16.1 - - - +
316F TYR* 3.9 19.2 + - + -
342F MET* 3.4 33.5 - - + +
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Residues in contact with ILE 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F VAL* 5.9 0.2 - - - -
10F THR 3.5 6.3 - - - +
12F ILE* 3.9 20.4 - - + -
121F ILE* 3.8 41.1 - - + -
123F GLY 4.0 0.2 - - - +
124F LYS 3.8 22.9 - - - +
126F GLN 4.0 8.3 - - - +
127F VAL* 3.6 24.7 - - + -
141F THR* 3.9 8.1 - - + +
143F ASN* 1.3 79.0 - - - +
145F LEU* 1.3 66.3 + - - +
146F ILE* 4.5 3.4 - - + -
314F ASN 3.0 7.8 + - - +
315F ILE* 3.5 16.5 - - + -
316F TYR* 2.8 30.2 + - - -
342F MET* 6.3 0.2 - - - -
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Residues in contact with LEU 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F VAL* 4.8 6.7 - - + -
10F THR 2.7 15.1 + - - +
11F VAL* 3.3 22.2 - - + +
12F ILE 2.8 31.7 + - - -
21F ALA* 3.4 33.0 - - + -
144F ILE* 1.3 75.3 - - - +
146F ILE* 1.3 61.0 - - - +
147F ALA 3.5 0.3 + - - -
316F TYR* 3.6 26.7 - - + -
318F ILE* 3.9 26.9 - - + -
335F GLY 5.0 0.9 - - - +
338F CYS* 3.8 13.2 - - - -
339F VAL* 4.2 15.5 - - + -
342F MET* 5.5 3.6 - - - -
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Residues in contact with ILE 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F ILE* 4.3 5.2 - - + -
121F ILE* 4.1 11.7 - - + -
144F ILE* 4.5 2.7 - - + -
145F LEU* 1.3 72.0 - - - +
147F ALA* 1.3 61.3 + - - +
148F THR* 3.7 14.1 - - + +
287F LEU* 3.5 36.1 - - + -
289F LEU* 4.0 13.5 - - + -
294F ILE* 5.2 0.4 - - + -
302F ILE* 3.6 28.9 - - + -
310F THR* 4.8 4.5 - - + -
315F ILE* 3.8 22.9 - - + -
316F TYR 2.6 21.8 + - - +
317F ALA* 3.1 5.0 - - + +
318F ILE* 2.9 29.8 + - - +
321F VAL* 4.1 3.8 - - + +
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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