Contacts of the strand formed by residues 161 - 170 (chain A) in PDB entry 1SZ7
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 161 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A LEU 3.7 0.7 - - - +
106A ILE* 3.6 2.6 - - - -
107A LEU* 2.8 49.9 + - + +
109A ASN 2.7 26.3 + - - +
110A ASN* 3.7 11.9 - - - +
150A PHE* 3.5 31.9 - - + -
152A GLN 3.4 7.9 - - - +
153A ASP* 3.7 1.7 - - - -
154A THR* 3.1 23.0 + - - +
160A VAL* 1.3 73.2 - - - +
162A GLU* 1.3 62.7 + - - +
163A ILE* 4.3 0.4 - - + -
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Residues in contact with GLU 162 (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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95A ASN* 3.8 10.2 + - - +
104A SER* 2.5 32.3 + - - +
105A LEU 3.3 3.4 - - - +
106A ILE* 3.6 23.5 - - + +
150A PHE* 3.4 4.7 - - - -
151A VAL* 2.8 51.6 + - + +
152A GLN* 2.9 43.7 + - + +
161A THR* 1.3 74.3 - - - +
163A ILE* 1.3 63.6 + - - +
164A ARG* 4.5 3.1 + - - -
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Residues in contact with ILE 163 (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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83A PHE* 4.4 22.4 - - + -
104A SER* 3.4 1.7 - - - -
105A LEU* 2.8 48.9 + - + +
107A LEU* 4.5 15.0 - - + -
131A LEU* 4.5 10.3 - - + -
132A CYS* 4.6 3.4 - - - -
135A LEU* 4.1 25.1 - - + -
148A ALA* 4.3 2.0 - - + -
149A LYS 3.4 16.4 - - - +
150A PHE* 3.7 41.3 - - + -
162A GLU* 1.3 74.1 - - - +
164A ARG* 1.3 68.0 + - - +
165A MET* 3.9 7.9 + - + -
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Residues in contact with ARG 164 (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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95A ASN* 2.8 34.9 + - - +
96A TRP 4.7 0.2 - - - -
97A SER* 4.2 8.9 - - - +
102A GLU* 3.1 44.8 + - - +
103A PHE 3.4 12.6 - - - -
104A SER* 2.9 24.5 + - - -
147A GLU* 3.7 2.5 - - - +
148A ALA* 3.4 3.8 - - - -
149A LYS* 2.8 45.7 + - + +
151A VAL* 4.0 27.1 - - + +
162A GLU* 4.0 4.9 + - - -
163A ILE* 1.3 72.5 - - - +
165A MET* 1.3 62.5 + - - +
166A ARG* 5.8 1.8 - - + -
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Residues in contact with MET 165 (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 PHE* 4.1 5.3 - - + -
78A ILE* 4.2 4.9 - - + -
102A GLU* 3.3 5.5 - - - +
103A PHE* 2.8 67.3 + - + +
105A LEU* 4.1 9.6 - - + -
135A LEU* 3.8 38.8 - - + -
139A LEU* 3.6 31.2 - - + -
146A VAL* 3.9 15.9 - - + -
147A GLU 3.3 1.6 - - - -
148A ALA* 3.8 19.1 - - + -
163A ILE* 3.9 8.7 + - + +
164A ARG* 1.3 76.5 - - - +
166A ARG* 1.3 60.2 + - - +
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Residues in contact with ARG 166 (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 PHE* 4.1 2.9 - - - -
101A ASP* 3.5 6.1 - - - +
102A GLU* 3.2 37.0 - - + +
146A VAL* 3.2 7.0 - - - +
147A GLU* 2.8 76.5 + - + +
164A ARG* 4.3 2.0 - - + -
165A MET* 1.3 75.2 - - - +
167A PHE* 1.3 69.3 + - - +
168A ILE* 3.6 33.1 + - - +
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Residues in contact with PHE 167 (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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69A HIS 5.4 1.8 - - - -
71A PHE* 3.5 30.0 - + + -
101A ASP* 2.8 34.7 + - + +
144A MET* 3.7 41.5 - - + -
145A ALA 4.0 6.1 - - - -
146A VAL* 4.3 1.3 - - + -
166A ARG* 1.3 80.7 + - - +
168A ILE* 1.3 62.9 + - - +
169A ARG* 3.4 39.9 - - - -
170A ARG* 3.4 11.4 - - + -
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Residues in contact with ILE 168 (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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145A ALA* 2.8 21.0 + - + +
146A VAL* 3.7 27.1 - - - +
147A GLU* 3.8 4.9 - - + +
166A ARG* 3.7 42.6 - - - +
167A PHE* 1.3 81.5 - - - +
169A ARG* 1.3 76.7 + - + +
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Residues in contact with ARG 169 (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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145A ALA* 2.9 41.7 + - + +
167A PHE* 3.4 15.8 - - - -
168A ILE* 1.3 93.1 - - + +
170A ARG* 1.3 78.1 + - - +
171A ILE* 3.8 30.3 - - - +
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Residues in contact with ARG 170 (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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69A HIS* 3.4 56.9 + - - +
143A GLN* 3.5 24.7 - - - +
144A MET* 5.4 1.8 - - - -
167A PHE* 3.4 14.1 - - + -
169A ARG* 1.3 95.0 + - - +
171A ILE* 1.3 70.1 + - - +
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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