Contacts of the strand formed by residues 156 - 166 (chain A) in PDB entry 3SJ5
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 156 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A LEU* 3.7 26.0 - - + -
95A LEU* 5.3 1.6 - - + -
145A ILE* 3.8 19.7 - - + +
146A GLU* 5.4 1.8 - - + -
149A SER* 3.7 26.5 + - - +
154A GLU 4.0 0.7 - - - +
155A GLU* 1.3 80.8 - - - +
157A SER* 1.3 60.9 + - - +
158A VAL* 3.8 25.1 - - + +
176A ILE* 3.9 11.7 - - + -
177A LYS 3.3 9.9 - - - +
178A PHE* 3.8 22.7 - - + -
179A LYS* 3.6 8.6 + - - +
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Residues in contact with SER 157 (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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156A ILE* 1.3 74.4 + - - +
158A VAL* 1.3 62.7 + - - +
159A GLU 4.2 0.2 - - - -
175A ARG 3.6 1.2 - - - +
176A ILE* 3.4 4.9 - - - +
177A LYS* 2.9 46.9 + - - +
179A LYS* 3.2 18.3 + - - -
62B ASN* 3.9 24.4 + - - +
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Residues in contact with VAL 158 (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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68A ARG* 6.3 0.9 - - - +
142A LEU* 4.7 11.0 - - + -
145A ILE* 4.1 15.5 - - + -
146A GLU* 5.5 10.1 - - + +
156A ILE* 3.8 27.6 - - + -
157A SER* 1.3 79.3 - - - +
159A GLU* 1.3 63.0 + - - +
160A GLU 4.3 1.2 + - - +
174A VAL* 4.0 31.6 - - + -
175A ARG 3.5 3.1 - - - +
176A ILE* 4.3 5.4 - - + -
62B ASN* 4.5 11.9 + - - +
64B ASN* 5.0 2.3 + - - -
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Residues in contact with GLU 159 (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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157A SER 4.2 0.2 - - - -
158A VAL* 1.3 73.6 - - - +
160A GLU* 1.3 73.7 + - - +
161A VAL* 3.5 7.3 + - + +
174A VAL* 3.2 4.5 - - - -
175A ARG* 2.8 62.1 + - + +
64B ASN* 3.6 31.0 + - - +
136B LYS* 6.0 2.1 - - - +
163B ARG* 5.6 1.6 - - - +
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Residues in contact with GLU 160 (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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142A LEU* 4.1 8.8 - - + +
158A VAL* 4.2 2.2 + - - +
159A GLU* 1.3 80.0 - - - +
161A VAL* 1.3 61.0 + - - +
162A GLU 4.2 3.4 - - - +
163A ARG* 2.8 57.2 + - - +
172A LEU* 4.0 17.1 - - + +
173A LYS 3.9 9.4 - - - +
174A VAL* 4.1 6.5 - - + +
138B TYR* 5.0 2.1 - - - -
160B GLU* 4.0 7.3 - - - +
163B ARG* 3.0 52.5 + - - +
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Residues in contact with VAL 161 (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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128A GLU* 4.4 13.7 - - - +
159A GLU* 3.9 17.9 - - + +
160A GLU* 1.3 76.5 - - - +
162A GLU* 1.3 74.2 + - + +
173A LYS* 2.8 28.7 + - + +
174A VAL 4.3 1.8 - - - -
175A ARG* 4.0 21.8 - - + +
138B TYR* 4.9 2.4 + - - -
163B ARG* 3.8 15.9 - - - +
164B GLY* 4.0 6.2 - - - -
165B GLU* 4.6 8.2 - - + +
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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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130A GLU* 4.6 5.0 - - - +
160A GLU* 3.9 2.2 - - - +
161A VAL* 1.3 95.0 - - + +
163A ARG* 1.3 63.0 + - - +
171A ARG 4.5 0.7 - - - -
172A LEU* 3.3 6.7 - - - +
173A LYS* 2.9 65.0 + - + +
163B ARG* 3.3 13.5 - - - +
164B GLY* 4.4 6.7 - - - -
165B GLU* 5.2 7.5 + - + +
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Residues in contact with ARG 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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138A TYR* 3.4 45.0 - - + +
139A ASP* 5.0 9.3 + - - -
142A LEU* 4.0 11.1 - - - +
160A GLU* 2.8 44.3 + - - +
162A GLU* 1.3 76.0 - - - +
164A GLY* 1.3 60.6 + - - +
171A ARG 3.3 6.5 - - - +
172A LEU* 3.8 14.0 - - + +
159B GLU* 5.6 1.8 - - - +
160B GLU* 2.9 51.2 + - - +
161B VAL 3.8 11.4 - - - +
162B GLU* 3.3 6.2 - - - +
163B ARG* 2.9 36.7 + - + +
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Residues in contact with GLY 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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138A TYR* 3.7 5.6 + - - -
163A ARG* 1.3 78.8 - - - +
165A GLU* 1.3 66.9 + - - -
166A LYS* 5.5 0.2 - - - -
171A ARG* 2.8 37.5 + - - +
161B VAL 4.0 10.5 - - - -
162B GLU* 4.5 8.3 - - - -
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Residues in contact with GLU 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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134A LYS 5.6 0.3 - - - +
136A LYS* 3.3 25.3 + - - -
138A TYR* 4.2 4.9 - - - +
164A GLY* 1.3 78.1 - - - -
166A LYS* 1.3 66.6 + - - +
168A GLY* 5.1 4.8 - - - +
169A PHE 3.1 9.6 + - - +
170A SER* 3.4 27.1 + - - +
161B VAL 6.0 0.4 - - - +
162B GLU* 5.1 5.8 + - - +
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Residues in contact with LYS 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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164A GLY 4.2 0.4 + - - -
165A GLU* 1.3 77.8 - - - +
167A ASP* 1.3 95.0 + - - +
168A GLY 3.0 2.2 - - - +
169A PHE* 2.7 34.9 + - - +
171A ARG* 4.3 22.9 + - - +
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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