Contacts of the strand formed by residues 5 - 12 (chain F) in PDB entry 1ZMD
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 ILE 5 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4F PRO* 1.3 81.3 - - - +
6F ASP* 1.3 64.6 + - - +
31F LYS* 5.2 5.4 - - - +
33F VAL* 4.1 18.2 - - + -
113F VAL* 4.5 10.1 - - + -
115F VAL* 4.2 16.2 - - + -
137F GLN* 3.9 15.0 - - - +
138F VAL 3.1 5.6 + - - +
139F ILE* 3.2 35.0 - - + -
140F ASP* 2.8 28.0 + - - +
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Residues in contact with ASP 6 (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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5F ILE* 1.3 77.9 - - - +
7F ALA* 1.3 63.9 + - - +
31F LYS* 2.9 40.6 + - - +
33F VAL* 4.8 0.3 - - - +
139F ILE* 4.7 1.1 - - - -
140F ASP* 3.0 17.9 - - + +
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Residues in contact with ALA 7 (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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6F ASP* 1.3 79.2 + - - +
8F ASP* 1.3 64.2 + - - +
9F VAL 4.0 4.5 - - - +
10F THR* 3.8 17.9 - - - +
31F LYS* 3.6 19.5 - - + +
33F VAL* 3.8 24.5 - - + -
139F ILE* 4.1 2.7 - - + -
140F ASP 2.9 5.7 + - - +
141F THR* 3.1 4.7 - - - +
142F LYS* 3.1 23.2 + - - +
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Residues in contact with ASP 8 (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* 1.3 76.0 - - - +
9F VAL* 1.3 59.6 + - - +
29F GLY 4.3 2.4 - - - +
30F PHE* 3.7 26.0 - - + -
31F LYS* 2.7 39.6 + - - +
141F THR* 3.7 1.6 - - - -
142F LYS* 2.9 39.7 + - + +
143F ASN* 2.9 37.2 + - - +
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Residues in contact with VAL 9 (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* 4.0 1.4 - - - +
8F ASP* 1.3 85.0 - - - +
10F THR* 1.3 66.5 + - - +
11F VAL* 4.1 20.6 - - + -
25F ALA* 4.4 11.0 - - + -
30F PHE* 3.9 26.5 - - + -
31F LYS 3.0 7.1 + - - +
32F THR* 3.3 12.1 - - + +
33F VAL 2.9 24.4 + - - +
141F THR* 3.8 0.2 - - - -
143F ASN* 3.6 11.0 - - + +
145F LEU* 4.8 4.0 - - + -
339F VAL* 5.2 1.8 - - + -
342F MET* 3.8 35.4 - - + -
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Residues in contact with THR 10 (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* 3.8 3.1 - - - +
9F VAL* 1.3 74.8 - - - +
11F VAL* 1.3 58.7 + - - +
12F ILE* 4.0 1.9 + - + +
33F VAL* 3.3 16.7 - - + +
35F ILE* 3.5 31.2 - - + -
127F VAL* 4.3 15.3 - - + -
139F ILE* 3.2 16.2 - - + +
141F THR* 3.1 32.7 + - - -
143F ASN 3.0 6.9 + - - -
144F ILE* 3.5 5.4 - - - +
145F LEU 2.8 29.2 + - - +
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Residues in contact with VAL 11 (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* 4.1 18.4 - - + -
10F THR* 1.3 73.4 - - - +
12F ILE* 1.3 64.2 + - - +
13F GLY 3.5 7.8 + - - +
18F GLY* 3.4 36.1 - - - +
21F ALA* 4.8 0.7 - - + -
22F ALA* 4.1 22.4 - - + +
32F THR* 4.5 1.1 - - + -
33F VAL 2.8 14.8 + - - +
34F CYS* 3.4 5.7 - - - -
35F ILE* 2.7 29.1 + - - +
145F LEU* 3.3 25.8 - - + +
147F ALA* 4.1 6.7 - - + -
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Residues in contact with ILE 12 (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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10F THR 4.5 2.5 - - - +
11F VAL* 1.3 74.8 - - - +
13F GLY* 1.3 57.4 + - - +
35F ILE* 3.9 16.2 - - + -
119F GLY* 4.5 6.3 - - - -
121F ILE* 3.9 21.1 - - + -
127F VAL* 4.0 15.7 - - + -
144F ILE* 4.0 15.9 - - + -
145F LEU 2.7 16.2 + - - +
146F ILE* 4.7 3.6 - - + -
147F ALA* 2.9 30.4 + - - -
148F THR* 3.4 12.7 + - + +
287F LEU* 3.7 21.3 - - + -
480F FAD 3.5 38.6 - - + +
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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