Contacts of the strand formed by residues 155 - 161 (chain B) in PDB entry 4F2N
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 GLY 155 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B ASN* 3.8 2.0 - - - -
153B GLY 4.0 0.6 + - - -
154B SER* 1.3 78.0 - - - +
156B TRP* 1.3 60.8 + - - -
173B THR 3.3 12.1 - - - -
175B ASN 3.5 9.4 - - - -
191B ASP* 3.6 1.4 - - - +
192B VAL* 2.8 37.1 + - - +
193B TRP* 3.2 19.8 + - - +
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Residues in contact with TRP 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B GLN* 2.9 26.2 + - - -
107B ASN* 3.3 52.1 - - + +
108B HIS* 3.5 26.0 - + - -
111B PHE* 4.0 11.9 - - + -
151B ASN* 3.5 3.7 + - - +
155B GLY* 1.3 73.4 - - - -
157B THR* 1.3 61.9 + - - +
158B TRP* 3.2 26.5 - + + +
172B SER* 3.3 2.9 - - - -
173B THR* 2.8 34.6 + - - +
175B ASN 3.2 20.8 + - - -
177B GLY 4.1 6.1 - - - -
189B THR* 3.5 17.0 - - + +
190B ALA 3.5 5.8 - - - -
191B ASP* 3.3 52.5 - - + -
192B VAL* 4.2 0.4 - - - -
193B TRP* 3.6 4.6 - - - +
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Residues in contact with THR 157 (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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144B PHE* 3.4 47.3 - - + +
147B ALA* 4.1 6.3 - - + -
148B GLY* 3.2 26.8 - - - +
151B ASN* 4.5 0.9 + - - -
156B TRP* 1.3 75.4 - - - +
158B TRP* 1.3 64.6 + - - +
170B ILE* 4.1 3.4 - - + -
171B ASP 3.6 5.2 - - - +
172B SER* 3.4 17.1 + - - +
189B THR* 3.1 4.2 + - - -
190B ALA* 2.8 37.0 + - - -
192B VAL* 4.2 6.6 - - - +
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Residues in contact with TRP 158 (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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106B PHE* 4.4 9.6 - + - -
107B ASN* 3.2 36.1 - - + -
110B PHE* 4.0 10.8 - + - -
144B PHE* 3.8 5.1 - - - -
156B TRP* 3.2 30.0 - - + +
157B THR* 1.3 74.8 - - - +
159B LEU* 1.3 59.4 + - - +
160B CYS* 3.8 15.5 - - - -
170B ILE* 3.3 10.2 - - - +
171B ASP* 2.8 45.6 + - + +
173B THR* 3.0 25.5 + - + -
177B GLY 3.8 6.7 - - - -
178B CYS* 4.6 0.2 - - - -
179B PRO* 3.2 32.7 - - + +
186B PRO* 3.7 30.7 - - + -
188B PHE 3.4 7.2 - - - -
189B THR* 3.4 28.0 - - - -
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Residues in contact with LEU 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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130B ILE* 4.3 20.6 - - + -
134B PHE* 4.0 22.0 - - + -
140B PHE* 3.6 42.0 - - + -
144B PHE* 4.0 2.8 - - + -
158B TRP* 1.3 73.0 - - - +
160B CYS* 1.3 60.5 + - - +
168B LEU* 4.2 6.3 - - + -
169B LEU 3.4 18.6 - - - +
170B ILE* 4.5 0.4 - - + +
186B PRO* 3.7 1.9 - - - +
187B ILE* 2.8 51.6 + - + +
188B PHE* 2.9 27.3 + - + +
218B TRP* 5.3 1.6 - - + -
221B VAL* 5.0 3.6 - - + -
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Residues in contact with CYS 160 (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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158B TRP* 3.8 9.9 - - - -
159B LEU* 1.3 78.3 - - - +
161B VAL* 1.3 65.0 + - - +
162B ASP 4.1 0.3 + - - -
167B GLU 3.7 0.2 - - - +
168B LEU* 3.2 9.2 - - - +
169B LEU* 2.8 42.2 + - + +
171B ASP* 4.9 3.1 - - - -
179B PRO* 3.7 37.2 - - - -
184B LEU* 3.9 25.6 - - + -
185B ARG 3.4 7.9 - - - +
186B PRO* 3.8 17.3 - - - -
187B ILE* 4.4 0.9 - - - +
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Residues in contact with VAL 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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160B CYS* 1.3 75.2 - - - +
162B ASP* 1.3 75.6 + - - +
163B PRO* 3.5 4.6 - - + +
166B LYS* 4.7 2.5 - - - -
167B GLU 3.4 6.7 - - - +
168B LEU* 3.7 21.8 - - + -
184B LEU* 3.8 2.9 - - - -
185B ARG* 2.8 36.6 + - + +
187B ILE* 3.8 18.4 - - + +
225B TYR* 3.9 5.2 - - + -
228B ALA* 3.9 24.5 - - + +
229B THR* 3.6 35.2 - - + -
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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