Contacts of the strand formed by residues 179 - 184 (chain A) in PDB entry 1F1J
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 179 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A PHE* 3.6 7.4 - - + -
166A PHE* 3.6 33.0 + - + +
168A GLY* 4.8 8.3 - - - +
174A LEU* 3.0 38.2 + - + -
175A LEU* 4.4 8.9 - - - +
176A GLU 4.5 1.2 - - - +
177A LYS 3.0 22.4 + - - -
178A PRO* 1.3 72.8 - - - +
180A LEU* 1.3 62.3 + - - +
181A PHE* 3.9 22.1 - - + -
217A ALA 3.3 20.6 + - - -
218A ASP* 2.8 16.1 + - - +
219A PHE* 3.4 19.3 - - + -
220A LEU 3.0 24.9 + - - +
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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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106A PHE* 4.4 14.4 - - + -
136A CYS* 4.7 3.1 - - - -
137A PHE* 2.8 17.2 + - - +
138A ALA* 3.2 2.9 - - + +
139A CYS* 2.8 26.9 + - - +
178A PRO* 4.0 13.9 - - + +
179A LYS* 1.3 79.3 - - - +
181A PHE* 1.3 65.4 + - - +
182A PHE* 3.8 27.0 - - + -
220A LEU* 3.6 26.9 - - + +
258A ILE* 5.3 3.6 - - + -
295A LEU* 4.8 1.8 - - + -
299A LEU* 3.7 33.2 - - + -
301A PHE* 4.1 21.3 - - + -
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Residues in contact with PHE 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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123A LEU* 3.8 24.7 - - + -
137A PHE* 4.1 7.0 - + - -
139A CYS* 3.1 29.2 - - + +
141A LEU* 5.4 5.2 - - + -
162A LEU* 6.1 0.4 - - + -
163A THR* 3.7 25.8 - - + -
166A PHE* 3.7 26.2 - + - -
179A LYS* 3.9 16.8 - - + -
180A LEU* 1.3 76.5 - - - +
182A PHE* 1.3 56.9 + - - +
183A ILE* 3.8 12.1 - - + +
219A PHE* 3.7 24.0 - + - -
220A LEU* 3.0 7.3 + - - +
221A PHE* 3.3 30.9 - + + -
222A ALA* 2.8 31.0 + - - +
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Residues in contact with PHE 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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101A PHE* 3.7 26.2 - + - -
138A ALA* 4.6 2.2 - - + -
139A CYS 3.0 11.3 + - - -
140A ILE* 3.4 31.9 - - + +
141A LEU 2.9 26.3 + - - +
180A LEU* 3.8 36.3 - - + -
181A PHE* 1.3 74.1 - - - +
183A ILE* 1.3 60.9 + - - +
184A GLN 4.0 0.2 + - - -
220A LEU* 5.6 3.1 - - + -
222A ALA* 3.4 29.4 - - + +
241A PHE* 4.6 8.3 - + + -
245A LEU* 3.8 30.5 - - + -
249A LEU* 5.7 0.9 - - + -
258A ILE* 4.7 13.9 - - + -
262A LEU* 4.2 13.2 - - + -
301A PHE* 5.7 1.3 - + - -
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Residues in contact with ILE 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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141A LEU* 3.7 34.5 - - + +
150A ILE* 4.5 6.1 - - + -
159A ILE* 4.6 15.3 - - + -
181A PHE* 3.8 26.9 - - + +
182A PHE* 1.3 76.7 - - - +
184A GLN* 1.3 59.8 + - - +
185A ALA* 3.7 20.7 + - + +
187A ARG* 6.5 0.2 - - + -
221A PHE* 4.4 8.3 - - + -
222A ALA 2.9 12.3 + - - +
223A TYR* 3.7 41.0 - - + +
224A SER* 3.0 27.9 + - - -
241A PHE* 4.8 2.2 - - - -
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Residues in contact with GLN 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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87A ARG* 3.9 9.0 - - - +
93A ASP* 5.0 0.2 - - - +
141A LEU 2.9 14.2 + - - +
142A LEU* 3.9 17.5 - - + -
143A SER 3.0 26.4 + - - +
182A PHE 4.0 1.6 + - - -
183A ILE* 1.3 68.0 - - - +
185A ALA* 1.3 62.0 + - - +
224A SER* 3.1 20.8 - - - -
231A SER* 3.1 25.0 + - - -
232A TRP 4.0 6.7 + - - +
239A SER* 3.3 31.0 - - - +
241A PHE* 3.3 18.3 + - + +
242A VAL* 4.5 6.1 - - + -
287A GLN* 5.0 0.2 + - - -
705C ASJ 2.8 25.9 + - - +
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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