Contacts of the strand formed by residues 156 - 161 (chain A) in PDB entry 1IJT
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 156 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A VAL* 4.0 33.0 - - + -
125A VAL* 4.0 7.2 - - + -
126A VAL 3.6 2.9 - - - -
151A PHE* 4.1 12.8 - - + -
152A THR 4.5 5.2 - - - +
153A ASP* 3.3 19.5 + - - +
154A GLU 3.5 2.3 - - - +
155A CYS* 1.3 80.5 - - - +
157A PHE* 1.3 70.2 + - - +
171A SER* 4.1 1.0 + - - -
172A TYR* 3.1 44.1 + - + +
173A LYS 4.6 0.5 + - - -
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Residues in contact with PHE 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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125A VAL* 3.3 5.5 - - - +
126A VAL* 2.8 42.6 + - + +
128A ILE* 4.2 14.1 - - + -
137A VAL* 3.3 32.5 - - + -
138A ALA 4.1 3.1 - - - -
139A MET* 4.0 32.8 - - + -
145A LEU* 4.6 0.4 - - + -
154A GLU 4.1 3.4 - - - -
155A CYS 3.7 14.1 - - - -
156A THR* 1.3 75.4 - - - +
158A LYS* 1.3 62.4 + - - +
159A GLU 3.5 1.0 + - - -
169A TYR* 4.3 19.5 - - + -
170A GLU 3.2 17.0 - - - +
171A SER* 3.7 18.8 - - - -
172A TYR* 4.2 0.7 - - - +
179A ILE* 3.8 34.8 - - + -
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Residues in contact with LYS 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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124A GLY 3.3 8.3 - - - +
125A VAL* 4.3 8.3 - - + +
157A PHE* 1.3 71.6 - - - +
159A GLU* 1.3 60.1 + - - +
160A ILE* 3.4 15.4 + - + +
168A ALA 3.4 6.4 - - - +
169A TYR* 3.4 2.2 - - - -
170A GLU* 2.8 56.8 + - + +
171A SER 5.5 0.4 - - - -
172A TYR* 3.8 40.8 - - + +
175A PRO* 6.1 3.9 - - - +
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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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118A LEU* 3.9 16.3 - - - +
124A GLY* 2.8 23.6 + - - +
126A VAL* 4.0 22.5 - - + +
157A PHE 3.5 1.8 + - - -
158A LYS* 1.3 69.0 - - - +
160A ILE* 1.3 61.6 + - - +
161A LEU 4.0 1.9 + - - -
167A ASN* 4.0 19.4 + - - +
168A ALA 3.7 3.4 - - - -
169A TYR* 2.7 44.2 + - + +
204A PRO* 5.5 0.5 - - - +
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Residues in contact with ILE 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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158A LYS* 3.9 14.8 - - + +
159A GLU* 1.3 76.0 - - - +
161A LEU* 1.3 72.8 + - - +
162A LEU* 3.7 7.9 - - + +
167A ASN* 3.2 5.0 - - - -
168A ALA* 2.8 43.6 + - + +
170A GLU* 3.5 36.8 - - + +
178A PHE* 4.3 12.6 - - + -
195A PRO* 6.3 0.7 - - + -
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Residues in contact with LEU 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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159A GLU 4.0 2.4 + - - -
160A ILE* 1.3 84.2 - - - +
162A LEU* 1.3 79.8 + - - +
165A ASN* 4.1 22.4 - - - +
166A TYR 3.6 8.3 - - - +
167A ASN* 3.4 14.4 + - - +
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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