Contacts of the strand formed by residues 136 - 143 (chain A) in PDB entry 1Z78
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 LYS 136 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A SER* 3.2 4.2 - - - -
76A LEU* 2.9 46.5 + - + +
129A LEU 3.7 23.3 + - - +
130A LEU* 4.0 17.5 - - + +
132A THR* 3.8 19.2 + - - +
134A GLN* 3.6 12.6 - - + +
135A TRP* 1.3 79.0 - - - +
137A SER* 1.3 60.5 + - - +
138A ILE* 5.4 0.2 - - + -
151A ILE* 3.9 20.4 - - + +
152A ASP* 3.7 25.7 + - - +
154A GLU* 5.9 0.4 + - - -
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Residues in contact with SER 137 (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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74A ALA 3.4 7.1 + - - -
75A SER* 4.2 8.4 + - - +
136A LYS* 1.3 72.9 - - - +
138A ILE* 1.3 68.3 + - - +
139A THR* 5.1 2.6 + - - -
151A ILE* 3.5 4.5 - - - +
152A ASP* 2.8 45.6 + - - +
212A LYS* 3.1 32.7 + - - +
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Residues in contact with ILE 138 (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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72A LEU* 4.5 7.2 - - + +
73A LEU* 3.4 5.2 - - - +
74A ALA* 2.8 44.8 + - + +
76A LEU* 3.9 12.3 - - + -
86A LEU* 4.3 20.6 - - + -
101A VAL* 5.5 0.9 - - + -
110A LEU* 4.1 17.9 - - + -
130A LEU* 3.9 29.6 - - + -
136A LYS* 5.0 0.7 - - + -
137A SER* 1.3 83.3 + - - +
139A THR* 1.3 68.0 + - - +
140A LEU* 4.5 10.5 - - + -
149A LEU* 3.9 21.3 - - + -
150A TYR 3.3 7.4 - - - +
151A ILE* 4.9 4.3 - - + -
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Residues in contact with THR 139 (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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71A LEU* 3.7 26.7 - - + -
72A LEU 3.6 2.7 - - - -
73A LEU* 4.3 16.3 - - + +
137A SER* 5.1 2.8 + - - -
138A ILE* 1.3 76.4 + - - +
140A LEU* 1.3 58.0 + - - +
148A GLN 3.5 4.3 - - - +
149A LEU* 3.6 1.5 - - - -
150A TYR* 2.8 52.1 + - + +
152A ASP 5.3 1.4 + - - -
205A PRO* 4.2 21.1 - - + +
208A ILE* 4.9 9.7 - - + +
209A LEU* 4.5 12.0 - - + +
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Residues in contact with LEU 140 (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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70A PHE* 3.9 6.8 - - + +
71A LEU* 3.3 3.9 - - - -
72A LEU* 2.7 64.9 + - + +
101A VAL* 4.5 4.9 - - + -
110A LEU* 4.0 21.5 - - + -
112A LEU* 4.0 26.9 - - + -
125A VAL* 5.1 2.2 - - + -
138A ILE* 4.0 6.7 - - + -
139A THR* 1.3 72.9 - - - +
141A PHE* 1.3 59.8 + - - +
142A VAL* 4.0 17.2 + - + -
147A ALA* 4.6 15.9 - - + -
148A GLN 3.6 14.4 - - - +
149A LEU* 4.1 16.4 - - + -
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Residues in contact with PHE 141 (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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67A GLU* 4.2 15.5 - - - -
70A PHE 3.6 14.1 - - - -
71A LEU* 3.5 24.0 - - + -
139A THR 3.9 0.6 + - - -
140A LEU* 1.3 71.6 - - - +
142A VAL* 1.3 62.6 + - - +
143A GLN* 3.6 42.4 - - + -
146A ARG 3.7 1.4 - - - +
147A ALA* 3.4 3.1 - - - -
148A GLN* 2.8 65.0 + - + +
150A TYR* 5.1 1.1 - - + -
203A THR 4.6 8.7 - - - -
204A THR* 5.5 5.4 - - + -
205A PRO* 4.0 29.2 - - + -
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Residues in contact with VAL 142 (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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67A GLU* 5.3 0.2 - - - +
69A GLY* 3.1 2.4 - - - -
70A PHE* 2.8 66.0 + - + +
99A PHE* 6.0 0.9 - - + -
112A LEU* 5.0 4.7 - - + -
140A LEU* 4.0 17.2 + - + -
141A PHE* 1.3 79.0 - - - +
143A GLN* 1.3 64.3 + - - +
144A GLU 4.3 3.8 - - - +
146A ARG 3.3 7.9 - - - +
147A ALA* 4.2 13.2 - - + -
161A LEU* 4.4 8.1 - - + -
165A ILE* 3.7 39.9 - - + -
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Residues in contact with GLN 143 (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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67A GLU* 4.9 12.8 + - + +
68A LYS* 3.6 9.6 - - + +
69A GLY* 5.6 0.2 - - - -
141A PHE* 3.6 35.4 - - + -
142A VAL* 1.3 73.3 - - - +
144A GLU* 1.3 72.5 + - + +
146A ARG* 2.9 61.6 + - + +
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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