Contacts of the strand formed by residues 156 - 161 (chain B) in PDB entry 2IGT
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 GLU 156 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B PRO* 4.4 19.4 - - + +
134B LEU 2.8 13.8 + - - +
135B LYS* 3.3 28.6 - - + +
136B VAL 2.8 25.6 + - - +
154B GLY 4.0 1.8 + - - +
155B ALA* 1.3 70.8 - - - +
157B VAL* 1.3 59.4 + - - +
158B THR* 4.2 0.5 + - - -
183B PRO* 3.8 22.0 - - + -
205B TYR* 5.7 0.7 - - - -
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Residues in contact with VAL 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B VAL* 3.3 15.9 - - + +
138B ASN* 4.9 2.2 - - + -
147B SER* 3.7 34.5 - - - +
150B ALA* 3.8 11.0 - - + -
151B ALA* 3.7 31.9 - - + +
155B ALA* 3.7 11.0 - - + +
156B GLU* 1.3 76.7 - - - +
158B THR* 1.3 71.2 + - - +
183B PRO 2.9 11.6 + - - +
184B ILE* 3.4 11.4 - - + -
185B ARG* 2.7 31.9 + - - +
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Residues in contact with THR 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B VAL 2.8 9.1 + - - +
137B LEU* 3.5 25.1 - - + +
138B ASN* 2.9 26.9 + - - +
156B GLU 4.2 0.7 + - - -
157B VAL* 1.3 74.6 + - - +
159B HIS* 1.3 60.9 + - - +
160B VAL* 4.1 1.1 - - + -
185B ARG* 2.7 42.7 + - - +
187B ILE* 3.7 27.4 - - + -
194B PHE* 3.9 7.9 - - + -
205B TYR* 3.7 10.0 - - - -
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Residues in contact with HIS 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B ASN* 3.6 10.5 - - - -
141B GLY* 3.3 29.6 + - - -
142B TYR 3.4 17.0 + - - -
144B GLY* 3.6 8.4 - - - -
147B SER* 2.7 32.1 - - - +
157B VAL 4.1 0.2 - - - -
158B THR* 1.3 73.0 - - - +
160B VAL* 1.3 59.9 + - - +
161B ASP* 4.0 6.7 - - + -
167B ILE* 3.7 21.0 - - + +
170B ALA* 4.2 1.1 - - + +
184B ILE* 4.3 6.1 - - + -
185B ARG 2.8 9.9 + - - +
186B TRP* 3.4 37.1 - + + -
187B ILE* 2.8 28.8 + - - +
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Residues in contact with VAL 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B LEU* 3.9 8.3 - - + -
138B ASN 2.9 10.3 + - - +
139B LEU* 3.7 20.0 - - + -
140B PHE 2.9 27.0 + - - -
141B GLY 3.0 7.6 + - - -
158B THR* 4.1 1.6 - - + -
159B HIS* 1.3 78.3 + - - +
161B ASP* 1.3 64.0 + - - +
187B ILE* 3.4 22.7 - - + -
189B GLU 3.7 19.3 - - - +
191B ALA* 4.1 20.0 - - + -
194B PHE* 3.6 36.6 - - + -
1002B SAM 4.7 0.4 + - - -
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Residues in contact with ASP 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B GLY 3.7 1.2 + - - -
142B TYR* 2.8 17.9 + - - -
159B HIS* 4.0 7.6 - - + -
160B VAL* 1.3 76.2 - - - +
162B ALA* 1.3 62.9 + - - +
163B SER* 2.9 23.7 + - - +
166B ALA* 4.0 7.6 - - + -
167B ILE* 3.8 20.4 - - + +
187B ILE 3.0 6.5 + - - +
188B CYS* 3.2 24.4 - - - +
189B GLU 3.7 4.3 - - - -
1002B SAM 2.6 57.8 + - - +
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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