Contacts of the strand formed by residues 183 - 192 (chain A) in PDB entry 1F4L
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 VAL 183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A LEU* 4.3 4.5 - - - -
128A TYR* 2.8 45.5 + - + +
130A PRO* 4.7 11.4 - - + -
181A THR* 4.1 12.1 - - + +
182A PRO* 1.3 80.8 - - - +
184A MET* 1.3 68.5 + - - +
185A ARG* 5.5 1.3 - - + -
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Residues in contact with MET 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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125A SER* 3.1 47.8 - - - +
126A GLN* 3.6 7.2 - - - -
127A LEU* 3.5 33.9 - - + +
168A THR* 3.8 23.6 - - + -
183A VAL* 1.3 80.2 - - - +
185A ARG* 1.3 58.6 + - - +
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Residues in contact with ARG 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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124A ILE 3.9 0.2 - - - +
125A SER* 3.4 2.3 - - - -
126A GLN 3.0 29.3 + - - +
128A TYR* 3.5 57.0 + - + -
135A PHE* 3.4 22.4 - - + -
183A VAL* 5.2 2.5 - - + -
184A MET* 1.3 74.4 - - - +
186A ASP* 1.3 74.8 + - - +
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Residues in contact with ASP 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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123A THR* 3.8 20.1 - - + +
124A ILE 3.3 3.9 - - - -
125A SER* 3.7 18.4 - - - -
135A PHE* 3.8 5.5 - - - -
185A ARG* 1.3 86.3 + - - +
187A SER* 1.3 65.2 + - - +
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Residues in contact with SER 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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123A THR* 3.9 4.7 - - - +
124A ILE* 2.9 32.3 + - - +
126A GLN* 6.4 0.4 - - - -
135A PHE* 3.7 16.8 - - - -
186A ASP* 1.3 78.8 - - - +
188A GLU* 1.3 62.5 + - - +
189A HIS* 3.4 13.0 - - - -
234A ASP* 2.7 29.5 + - - -
248A LYS* 3.0 15.5 + - - +
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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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121A ASN* 4.5 19.8 - - + +
122A ARG 3.9 7.2 - - - +
123A THR* 4.2 11.6 + - - +
187A SER* 1.3 74.3 + - - +
189A HIS* 1.3 70.6 + - - +
190A PHE* 3.9 22.0 - - + -
232A SER* 4.4 0.2 + - - -
248A LYS* 2.7 43.3 + - - +
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Residues in contact with HIS 189 (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 ASN* 3.4 5.4 - - - +
122A ARG 2.9 33.6 + - - +
124A ILE* 3.5 22.8 - - + +
126A GLN* 4.3 12.2 + - - -
187A SER* 3.4 27.8 + - - -
188A GLU* 1.3 78.3 - - - +
190A PHE* 1.3 63.8 + - - +
191A PHE* 3.6 22.3 - - + -
230A ASP* 2.7 29.1 + - - +
232A SER* 3.1 26.5 + - - +
233A ARG* 4.5 9.9 - - - -
234A ASP* 3.6 17.8 + - - -
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Residues in contact with PHE 190 (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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110A TYR* 3.5 25.1 - - + +
114A LYS* 5.1 8.5 - - - -
119A ILE* 4.0 12.3 - - + -
120A LYS 3.4 1.8 - - - -
121A ASN* 3.1 33.7 - - - -
188A GLU* 3.9 20.9 - - + -
189A HIS* 1.3 75.3 - - - +
191A PHE* 1.3 55.6 + - - +
230A ASP* 3.7 2.8 - - - -
231A ILE* 2.8 42.6 + - + +
232A SER* 3.0 28.0 + - - -
242A ILE* 4.1 9.6 - - + -
245A ALA* 4.0 29.6 - - + -
248A LYS* 4.2 15.7 - - + -
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Residues in contact with PHE 191 (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 PHE 3.6 0.2 - - - +
119A ILE* 3.4 7.7 - - - +
120A LYS* 2.7 46.7 + - + +
122A ARG* 3.3 54.7 - - + -
124A ILE* 4.0 11.4 - - + -
189A HIS* 3.6 29.4 - - + -
190A PHE* 1.3 77.2 - - - +
192A PHE* 1.3 62.3 + - - +
193A ASP 3.8 0.3 + - - -
228A GLN* 4.1 29.6 - - + +
229A TRP 3.1 5.6 - - - +
230A ASP* 3.5 39.9 - - + -
231A ILE* 4.4 2.2 - - - -
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Residues in contact with PHE 192 (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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113A LEU* 3.9 35.0 - - + -
118A PHE* 3.6 14.4 - - + -
119A ILE* 4.1 8.3 - - + -
191A PHE* 1.3 71.9 - - - +
193A ASP* 1.3 63.4 + - - +
194A LEU* 2.9 27.2 + - + -
197A PHE* 3.5 32.5 - + - -
228A GLN* 3.5 3.4 - - - -
229A TRP* 2.7 53.6 + + + +
231A ILE* 4.1 18.4 - - + +
254A LEU* 5.4 1.6 - - + -
304A PHE* 4.0 10.3 - + - -
307A ALA* 3.8 15.9 - - + -
308A MET* 3.7 22.4 - - + -
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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