Contacts of the strand formed by residues 178 - 188 (chain A) in PDB entry 2FK2
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 LYS 178 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A CYS* 3.7 31.9 - - + +
145A GLU* 3.4 21.3 - - - +
146A THR* 4.0 17.9 - - + +
173A PRO* 3.5 1.6 - - - +
174A CYS 2.9 32.5 + - - +
175A GLY* 5.9 1.3 - - - -
176A ILE 3.9 0.4 - - - +
177A ASP* 1.3 107.6 + - - +
179A PHE* 1.3 76.9 + - - +
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Residues in contact with PHE 179 (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 CYS* 3.6 2.3 - - - -
145A GLU 2.8 26.9 + - - -
146A THR 4.3 0.2 - - - -
147A HIS* 4.0 20.6 - - + -
150A TRP* 2.9 26.7 + - + +
170A MET* 3.3 45.3 - - + -
171A LEU 3.4 9.9 - - - +
172A LEU 3.6 7.2 - - - -
173A PRO* 3.9 21.5 - - + -
174A CYS* 4.2 0.9 - - - +
177A ASP 3.9 17.7 - - - -
178A LYS* 1.3 83.7 - - - +
180A ARG* 1.3 64.5 + - - +
181A GLY 4.2 1.3 - - - +
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Residues in contact with ARG 180 (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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139A GLU* 3.2 5.7 - - - +
140A ARG 2.9 40.6 + - - +
141A MET* 5.9 3.4 - - - +
143A VAL 3.6 19.3 - - - +
144A CYS* 3.7 19.1 - - - -
150A TRP* 3.3 10.8 - - - -
171A LEU 3.1 1.6 + - - -
172A LEU* 3.0 46.0 + - + +
173A PRO 2.7 27.5 + - - -
174A CYS* 3.7 11.3 - - - +
179A PHE* 1.3 71.4 - - - +
181A GLY* 1.3 56.6 + - - +
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Residues in contact with GLY 181 (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 GLN 3.1 13.0 - - - -
139A GLU* 3.8 4.5 - - - -
150A TRP* 3.5 19.4 - - - -
170A MET* 3.6 5.4 - - - +
171A LEU* 2.9 30.6 + - - +
179A PHE* 3.6 1.3 - - - +
180A ARG* 1.3 81.1 - - - +
182A VAL* 1.3 64.7 + - - +
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Residues in contact with VAL 182 (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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137A HIS* 3.6 1.6 - - - -
138A GLN* 2.8 39.2 + - + +
150A TRP* 3.7 42.2 - - + +
153A VAL* 4.7 2.9 - - + -
154A ALA* 4.4 2.5 - - + -
168A TYR* 4.0 24.7 - - + -
169A GLY 3.5 16.2 - - - +
170A MET* 4.3 4.5 - - + -
171A LEU* 3.8 7.1 - - - +
181A GLY* 1.3 75.1 - - - +
183A GLU* 1.3 70.3 + - - +
184A PHE* 3.9 21.6 - - + -
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Residues in contact with GLU 183 (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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135A PHE* 3.4 37.9 - - + -
136A LEU 3.3 6.1 - - - +
137A HIS* 4.7 6.5 + - - +
168A TYR* 3.2 2.1 - - - +
169A GLY* 2.8 46.2 + - - +
171A LEU* 4.1 22.9 - - + +
182A VAL* 1.3 73.5 - - - +
184A PHE* 1.3 61.4 + - - +
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Residues in contact with PHE 184 (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 3.7 0.3 - - - +
135A PHE* 3.4 6.7 - - - -
136A LEU* 2.9 58.2 + - + -
138A GLN* 3.8 20.6 - - + -
154A ALA* 3.7 21.3 - - + -
157A THR* 3.8 34.3 - - + -
158A CYS* 3.9 6.5 - - - -
165A LEU* 3.6 7.4 - - + -
167A ASP 3.5 14.4 - - - +
168A TYR* 3.7 7.2 - - + +
182A VAL* 3.9 30.3 - - + -
183A GLU* 1.3 79.5 - - - +
185A VAL* 1.3 65.1 + - - +
186A CYS* 3.8 24.7 - - - -
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Residues in contact with VAL 185 (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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133A CYS* 3.5 28.5 - - + -
134A LYS 3.3 6.7 - - - +
135A PHE* 4.1 21.5 - - + +
158A CYS* 4.4 0.7 - - - -
165A LEU* 3.7 4.2 - - - +
166A HIS* 2.9 32.1 + - + -
167A ASP* 3.1 18.9 + - + +
184A PHE* 1.3 82.1 - - - +
186A CYS* 1.3 64.8 + - - +
187A CYS* 3.9 8.3 - - - -
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Residues in contact with CYS 186 (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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132A ALA 4.6 0.2 - - - +
133A CYS* 3.1 2.8 - - - -
134A LYS* 2.8 39.8 + - + +
136A LEU* 3.9 14.8 - - + -
158A CYS* 2.0 53.6 - - - -
161A LYS* 5.1 3.8 - - + -
163A THR* 3.1 20.6 - - + +
164A ASN 3.5 1.6 - - - -
184A PHE* 3.8 17.9 - - - -
185A VAL* 1.3 71.9 - - - +
187A CYS* 1.3 61.2 + - - +
188A PRO* 4.5 0.2 - - - +
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Residues in contact with CYS 187 (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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133A CYS* 2.1 45.3 - - - -
163A THR* 3.2 6.2 - - - -
164A ASN* 2.8 38.0 + - + +
166A HIS* 4.0 22.7 - - + -
185A VAL* 3.9 11.0 - - - -
186A CYS* 1.3 74.9 - - - +
188A PRO* 1.3 72.5 - - + +
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Residues in contact with PRO 188 (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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131A GLU* 3.5 51.6 - - + +
132A ALA 3.6 21.5 - - - +
133A CYS* 4.1 2.9 - - - +
162A SER 4.9 0.7 - - - +
163A THR* 4.4 5.6 - - + -
164A ASN* 4.8 2.4 + - - +
187A CYS* 1.3 95.4 - - + +
189A LEU* 1.3 69.3 + - - +
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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