Contacts of the strand formed by residues 155 - 161 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A ASN* 4.0 2.7 - - - -
153A GLY 3.9 1.6 + - - -
154A SER* 1.3 76.8 - - - +
156A TRP* 1.3 68.7 + - - -
173A THR 3.2 12.3 - - - -
175A ASN 3.6 8.7 - - - -
191A ASP* 3.7 0.2 - - - +
192A VAL* 2.9 30.5 + - - +
193A TRP* 3.3 19.4 + - - +
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Residues in contact with TRP 156 (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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104A GLN* 3.0 20.6 + - - -
107A ASN* 3.4 54.2 - - + +
108A HIS* 3.5 30.7 - + - -
111A PHE* 4.0 10.5 - - + -
151A ASN* 3.1 5.7 + - - +
155A GLY* 1.3 79.0 - - - -
157A THR* 1.3 62.0 + - - +
158A TRP* 3.3 25.8 - + + +
172A SER* 3.4 0.2 - - - -
173A THR* 2.8 39.7 + - - +
175A ASN 3.2 16.1 + - - -
177A GLY 4.3 0.2 - - - -
189A THR* 3.5 18.8 - - + +
190A ALA 3.5 6.3 - - - -
191A ASP* 3.4 47.8 - - + -
192A VAL* 4.3 0.9 - - - -
193A TRP* 3.6 4.4 - + - +
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Residues in contact with THR 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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144A PHE* 3.4 32.6 - - + +
147A ALA* 4.0 9.9 - - + -
148A GLY* 3.3 35.0 - - - +
151A ASN* 3.5 6.6 + - - -
156A TRP* 1.3 73.8 - - - +
158A TRP* 1.3 63.0 + - - +
170A ILE* 4.2 4.7 - - + -
171A ASP 3.7 2.5 - - - -
172A SER* 3.0 22.2 + - - +
189A THR* 3.2 2.3 - - - -
190A ALA* 2.8 35.8 + - - -
192A VAL* 4.4 3.9 - - - +
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Residues in contact with TRP 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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106A PHE* 4.4 7.0 - + - -
107A ASN* 3.2 37.7 - - + -
110A PHE* 3.8 11.9 - + - -
144A PHE* 3.9 5.7 - - - -
156A TRP* 3.3 29.6 - - + +
157A THR* 1.3 76.0 - - - +
159A LEU* 1.3 59.3 + - - +
160A CYS* 3.7 16.2 - - - -
170A ILE* 3.3 9.4 - - - +
171A ASP* 2.8 48.4 + - - +
173A THR* 2.9 26.4 + - + -
177A GLY 3.9 3.8 - - - -
179A PRO* 3.2 32.8 - - + +
186A PRO* 3.5 32.1 - - + -
188A PHE 3.4 7.2 - - - +
189A THR* 3.3 28.9 - - + -
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Residues in contact with LEU 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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130A ILE* 4.4 21.3 - - + -
134A PHE* 3.7 21.5 - - + -
140A PHE* 3.7 40.2 - - + -
144A PHE* 4.0 3.4 - - + -
158A TRP* 1.3 72.7 - - - +
160A CYS* 1.3 60.9 + - - +
168A LEU* 4.1 11.2 - - + -
169A LEU 3.5 14.8 - - - +
170A ILE* 4.6 0.2 - - + -
186A PRO* 3.7 1.6 - - - +
187A ILE* 2.9 51.9 + - + +
188A PHE* 2.9 26.1 + - + +
218A TRP* 5.2 1.6 - - + -
221A VAL* 4.9 2.9 - - + -
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Residues in contact with CYS 160 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158A TRP* 3.7 22.0 - - - -
159A LEU* 1.3 78.6 - - - +
161A VAL* 1.3 64.7 + - - +
168A LEU* 3.2 9.7 - - - +
169A LEU* 2.8 44.9 + - + +
171A ASP* 4.4 10.1 - - - -
179A PRO* 3.8 27.1 - - - -
184A LEU* 4.1 16.6 - - + -
185A ARG 3.4 7.4 - - - +
186A PRO* 3.9 7.9 - - - -
187A ILE* 4.4 0.7 - - - +
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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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160A CYS* 1.3 75.4 - - - +
162A ASP* 1.3 72.3 + - - +
163A PRO* 3.4 8.7 - - + +
166A LYS* 4.4 5.4 - - - -
167A GLU 3.3 7.9 - - - +
168A LEU* 3.7 21.5 - - + -
169A LEU* 4.5 0.4 - - - -
184A LEU* 3.9 2.3 - - - -
185A ARG* 2.8 36.0 + - + +
187A ILE* 4.0 7.8 - - + +
225A TYR* 3.9 18.2 - - + -
228A ALA* 3.9 31.4 - - + +
229A THR* 3.7 21.5 - - + -
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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