Contacts of the strand formed by residues 178 - 188 (chain A) in PDB entry 1F6O
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 CYS 178 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A ALA* 3.9 3.2 - - - +
126A ALA* 3.8 0.7 - - - -
127A TYR* 2.9 41.4 + - - +
149A MET* 3.5 36.8 - - + -
157A TYR* 4.9 1.1 - - + -
169A ASN* 4.1 26.5 - - + -
170A ILE 3.2 17.0 - - - +
171A SER* 3.7 7.6 - - - +
172A SER* 3.6 6.4 + - - +
177A ALA* 1.3 77.7 - - - +
179A VAL* 1.3 67.6 + - - +
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Residues in contact with VAL 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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95A ALA* 3.7 23.1 - - - +
98A LEU* 3.6 28.9 - - + -
99A ALA* 3.7 17.7 - - + +
102A PHE* 3.5 31.2 - - + -
124A THR* 4.1 4.5 - - + -
125A GLU 3.3 10.1 - - - +
168A MET 4.1 0.2 - - - +
169A ASN* 3.0 8.0 - - - -
170A ILE* 2.7 39.2 + - - +
178A CYS* 1.3 78.7 - - - +
180A LEU* 1.3 72.7 + - - +
181A LEU* 4.8 0.2 - - + -
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Residues in contact with LEU 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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124A THR* 3.2 9.0 - - - -
125A GLU* 2.8 61.0 + - + +
127A TYR* 3.9 10.3 - - + -
159A TYR* 5.8 0.2 - - - +
167A CYS* 4.2 11.2 - - + -
168A MET 3.3 24.2 - - - +
169A ASN* 3.3 23.1 - - - +
179A VAL* 1.3 75.0 - - - +
181A LEU* 1.3 75.5 + - - +
182A ARG* 3.7 16.1 + - + +
218A PRO* 4.5 7.2 - - + -
7D YRR 3.7 24.5 - - + -
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Residues in contact with LEU 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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102A PHE* 4.0 15.5 - - + -
107A LEU* 3.9 19.5 - - + -
121A ILE* 3.8 36.1 - - + -
123A GLU 3.9 2.7 - - - +
124A THR* 4.5 1.8 - - + -
168A MET* 3.1 41.9 + - + +
170A ILE* 3.8 23.1 - - + -
180A LEU* 1.3 86.0 - - - +
182A ARG* 1.3 58.8 + - - +
183A ALA 5.1 0.4 - - - +
184A LEU* 4.6 8.3 - - + -
218A PRO* 3.5 16.5 - - - +
221A LEU* 3.7 17.7 - - + +
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Residues in contact with ARG 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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123A GLU* 2.5 52.2 + - + +
125A GLU* 2.9 41.0 + - + -
180A LEU* 3.9 23.7 - - + +
181A LEU* 1.3 75.6 - - - +
183A ALA* 1.3 63.0 + - - +
216A SER 4.0 0.2 - - - -
217A GLY* 2.7 30.7 + - - -
218A PRO* 2.9 19.6 - - + +
221A LEU* 3.6 5.2 - - - -
262A VAL* 3.4 23.9 - - - +
276A ARG* 4.3 0.7 - - - +
286A SER* 2.4 31.9 + - - -
287A VAL* 4.7 1.6 - - - +
7D YRR 5.0 2.0 + - - -
8D T 3.0 27.1 + - - -
9D T 4.8 2.2 + - - -
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Residues in contact with ALA 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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121A ILE* 3.8 0.9 - - - +
122A VAL* 2.9 33.3 + - + +
123A GLU* 3.3 24.8 + - + +
182A ARG* 1.3 83.4 - - - +
184A LEU* 1.3 70.5 + - - +
215A CYS 3.2 8.5 - - - +
217A GLY 4.2 1.8 - - - +
221A LEU* 3.6 2.3 - - - +
284A TRP 3.4 23.8 - - - +
286A SER 4.0 3.8 - - - +
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Residues in contact with LEU 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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107A LEU* 4.0 10.5 - - + -
119A GLY* 4.2 20.0 - - - +
120A ARG 3.2 3.8 - - - +
121A ILE* 3.5 35.7 - - + +
122A VAL* 4.3 4.5 - - - -
181A LEU* 4.6 9.9 - - + -
183A ALA* 1.3 82.1 - - - +
185A GLU* 1.3 59.7 + - - +
186A PRO* 3.4 11.0 - - - +
215A CYS* 3.2 29.8 + - + +
216A SER 4.6 0.2 + - - -
221A LEU* 4.0 29.4 - - + -
225A LEU* 3.8 31.0 - - + -
284A TRP* 3.8 9.7 - - - +
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Residues in contact with GLU 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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119A GLY* 3.3 1.6 - - - -
120A ARG* 2.6 65.5 + - + +
122A VAL* 4.0 9.3 - - + +
184A LEU* 1.3 71.7 - - - +
186A PRO* 1.3 70.8 - - + +
187A LEU* 3.1 25.9 + - + +
284A TRP* 3.1 45.1 + - + +
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Residues in contact with PRO 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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118A ARG 4.1 5.2 - - - +
119A GLY* 4.5 0.9 - - - -
184A LEU 3.4 8.7 - - - +
185A GLU* 1.3 85.0 - - + +
187A LEU* 1.3 65.2 + - - +
190A LEU* 3.3 33.2 - - + +
193A MET* 4.1 12.3 - - + -
211A ASP 4.0 17.9 - - - +
214A LEU* 4.0 15.3 - - + -
215A CYS* 4.2 10.8 - - + +
284A TRP* 3.5 27.5 - - + -
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Residues in contact with LEU 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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106A VAL* 4.3 20.2 - - + -
118A ARG* 2.9 18.1 + - + +
119A GLY 4.4 1.3 - - - -
120A ARG* 3.7 30.3 - - + +
185A GLU* 3.4 39.0 - - - +
186A PRO* 1.3 76.1 - - - +
188A GLU* 1.3 72.8 + - + +
190A LEU* 3.7 7.9 - - - +
248A PRO* 6.4 0.4 - - + -
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Residues in contact with GLU 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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80A LYS* 3.2 33.6 + - - +
116A GLU* 4.2 10.7 - - - +
117A LEU* 3.3 6.1 - - - -
118A ARG* 3.0 56.3 + - + +
187A LEU* 1.3 91.5 - - + +
189A GLY* 1.3 61.7 + - - +
190A LEU* 3.5 4.9 - - - +
193A MET* 3.7 4.5 - - - +
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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