Contacts of the strand formed by residues 52 - 59 (chain A) in PDB entry 1Z9N
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 GLY 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A GLU* 4.9 0.2 - - - -
49A SER* 2.7 40.3 + - - -
50A ALA 3.7 0.4 - - - -
51A TYR* 1.3 80.1 - - - +
53A LEU* 1.3 66.9 + - - -
133A LEU* 3.6 3.3 - - - +
134A ALA 3.8 6.1 - - - -
135A PRO 4.2 3.1 - - - -
137A LEU 3.1 15.7 - - - -
138A LYS* 4.3 9.8 - - - +
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Residues in contact with LEU 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ILE* 4.1 10.3 - - + -
47A THR 3.3 6.7 - - - +
48A GLU* 3.6 31.0 - - + -
52A GLY* 1.3 72.8 - - - -
54A VAL* 1.3 61.5 + - - +
55A PHE* 3.9 14.4 - - + -
133A LEU* 3.5 1.9 - - - -
134A ALA* 2.8 31.1 + - - +
137A LEU* 2.9 39.7 + - + +
138A LYS 3.8 13.7 - - - +
139A LYS 3.8 15.9 - - - +
140A LEU* 3.9 6.5 - - + +
143A VAL* 3.8 30.3 - - + -
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Residues in contact with VAL 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A GLU 3.4 2.1 - - - +
46A ILE* 3.2 6.2 - - - +
47A THR* 2.8 46.8 + - - +
49A SER* 3.8 15.9 - - - -
53A LEU* 1.3 76.6 - - - +
55A PHE* 1.3 63.9 + - - +
56A THR* 3.6 19.1 - - - +
131A PRO* 4.0 4.0 - - + -
132A VAL 3.4 6.3 - - - +
133A LEU* 3.9 8.7 - - + -
108B TRP* 3.6 53.2 - - + +
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Residues in contact with PHE 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A VAL* 4.1 8.5 - - + -
45A GLU 3.6 2.9 - - - -
46A ILE* 3.7 37.9 - - + -
53A LEU* 3.9 22.2 - - + -
54A VAL* 1.3 75.4 - - - +
56A THR* 1.3 60.5 + - - +
57A PRO* 3.5 5.5 - - - +
69A PHE* 3.9 22.9 - + + -
71A ILE* 4.1 14.8 - - + -
117A LEU* 3.9 31.9 - - + -
131A PRO* 3.2 3.1 - - - +
132A VAL* 2.9 41.5 + - + +
134A ALA* 3.9 25.1 - - + -
137A LEU* 4.5 4.5 - - + -
143A VAL* 5.0 0.4 - - + -
148A LEU* 4.1 16.2 - - + -
176A ILE* 5.3 0.2 - - + -
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Residues in contact with THR 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A VAL* 3.9 1.5 - - - +
45A GLU* 2.7 38.6 + - - -
47A THR* 4.9 3.5 + - - +
54A VAL* 3.6 17.7 + - - +
55A PHE* 1.3 71.1 - - - +
57A PRO* 1.3 70.6 - - + +
58A LYS* 3.3 31.6 - - - +
129A THR 4.8 6.1 - - - +
131A PRO* 3.7 13.7 - - + +
106B TYR* 6.0 0.7 - - - +
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Residues in contact with PRO 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A THR 3.8 4.9 - - - +
44A VAL* 4.0 8.5 - - + -
55A PHE 3.5 7.2 - - - +
56A THR* 1.3 88.9 - - - +
58A LYS* 1.3 65.0 + - - +
59A LEU* 3.9 20.2 - - + -
69A PHE* 5.5 2.0 - - + -
120A LEU* 4.0 22.7 - - + -
121A PHE 5.9 0.2 - - - +
128A ALA* 3.3 21.0 - - + +
129A THR* 3.3 15.5 - - - +
130A THR 3.3 37.7 - - - +
132A VAL* 6.3 0.4 - - + -
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Residues in contact with LYS 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A GLY* 3.4 6.1 - - - -
43A THR* 2.8 39.4 + - - +
45A GLU* 2.7 52.9 + - + +
56A THR* 3.3 43.2 - - - +
57A PRO* 1.3 74.8 - - - +
59A LEU* 1.3 59.0 + - - +
60A HIS* 4.9 1.7 - - - -
128A ALA 3.6 2.2 - - - -
129A THR* 5.0 6.1 - - + -
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Residues in contact with LEU 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A VAL* 3.8 25.1 - - + -
41A VAL* 3.1 17.9 - - + +
43A THR 3.4 28.9 - - - +
44A VAL* 4.1 3.8 - - + -
57A PRO* 3.9 16.2 - - + -
58A LYS* 1.3 80.3 - - - +
60A HIS* 1.3 63.5 + - - +
62A LEU* 3.9 15.7 - - + -
120A LEU* 4.1 8.5 - - + -
126A GLY 4.4 0.2 - - - -
127A SER* 3.2 7.8 - - - -
128A ALA* 3.0 38.9 + - + +
129A THR* 5.2 1.0 - - - +
150A ILE* 3.6 28.5 - - + -
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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