Contacts of the strand formed by residues 181 - 189 (chain D) in PDB entry 5FLX
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 181 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13331 U 3.6 29.0 + - - +
13341 G 3.3 39.1 - - - +
14981 A 3.6 24.0 - - - +
14991 U 3.2 34.9 + - - +
140D GLY* 4.3 0.5 - - - -
174D HIS* 5.2 9.2 - - + +
175D VAL 3.2 10.8 - - - +
176D LEU* 4.6 7.2 - - + -
180D GLY* 1.3 74.3 - - - -
182D LEU* 1.3 63.3 + - - +
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Residues in contact with LEU 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13341 G 4.1 1.1 - - - -
109D LEU* 6.1 5.6 - - + -
115D VAL* 5.5 2.9 - - + -
138D VAL* 5.0 6.5 - - + -
139D SER 3.4 13.0 - - - +
140D GLY* 4.1 6.3 - - - -
141D LYS 4.2 17.0 - - - +
142D LEU* 3.6 33.9 - - + -
173D ARG 3.8 0.5 - - - +
174D HIS* 3.7 3.3 - - - -
175D VAL* 3.0 44.4 + - + +
177D LEU* 4.3 24.7 - - + -
179D GLN* 4.8 2.5 - - + -
180D GLY* 3.6 20.6 - - - +
181D VAL* 1.3 80.7 - - - +
183D GLY* 1.3 63.0 + - - +
184D ILE* 3.9 4.7 + - + +
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Residues in contact with GLY 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13341 G 3.3 32.0 + - - -
13351 G 4.0 10.8 - - - -
137D VAL 3.8 0.3 - - - +
138D VAL* 4.5 0.3 - - - +
139D SER* 3.0 34.0 + - - +
173D ARG 3.3 10.3 - - - -
174D HIS* 4.5 0.7 - - - -
182D LEU* 1.3 72.5 - - - +
184D ILE* 1.3 63.2 + - - +
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Residues in contact with ILE 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13351 G 4.7 0.2 + - - -
102D ALA* 3.8 37.4 - - + +
105D LEU* 4.4 16.6 - - + -
106D ARG* 5.2 2.0 - - + +
109D LEU* 4.6 15.3 - - + -
136D VAL* 5.5 1.1 - - + -
137D VAL 3.3 5.2 - - - +
138D VAL* 4.1 26.9 - - + -
171D ALA 3.5 12.8 - - - +
172D VAL* 3.9 3.8 - - - +
173D ARG* 3.2 31.3 + - + +
175D VAL* 4.7 13.7 - - + -
182D LEU* 4.4 9.4 - - + +
183D GLY* 1.3 79.2 - - - +
185D LYS* 1.3 63.8 + - - +
186D VAL* 4.0 5.2 + - + +
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Residues in contact with LYS 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13351 G 4.1 21.9 + - - +
13361 C 2.7 42.1 + - - -
135D GLU 3.5 2.6 - - - +
136D VAL* 3.3 5.3 - - - +
137D VAL* 2.8 60.0 + - + +
170D THR* 5.5 9.0 - - + -
171D ALA 3.9 4.9 - - - +
172D VAL* 4.3 19.5 - - + -
184D ILE* 1.3 75.6 - - - +
186D VAL* 1.3 62.0 + - - +
187D LYS* 3.9 12.6 - - - +
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Residues in contact with VAL 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D ALA* 3.3 32.5 - - + +
101D GLN* 4.6 7.9 - - + -
102D ALA* 3.8 30.7 - - + -
105D LEU* 5.0 8.7 - - + -
126D ILE* 4.6 6.5 - - + -
134D CYS* 4.6 1.1 - - - -
135D GLU 3.7 2.9 - - - -
136D VAL* 4.2 28.0 - - + -
169D ASP 3.3 11.4 - - - +
170D THR* 5.1 0.7 - - - -
171D ALA* 3.9 18.8 + - + +
184D ILE* 4.0 3.1 - - + -
185D LYS* 1.3 75.9 - - - +
187D LYS* 1.3 60.3 + - - +
188D ILE* 4.4 13.2 - - + -
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Residues in contact with LYS 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D CYS* 3.7 0.7 - - - -
135D GLU* 3.1 56.6 + - + +
137D VAL* 5.4 5.7 - - - +
157D MET* 3.3 22.6 - - + +
159D HIS* 3.9 20.5 + - + +
168D VAL* 4.0 17.9 - - + -
169D ASP 3.4 5.4 - - - +
170D THR* 4.3 15.2 + - + +
185D LYS* 5.3 14.9 - - - +
186D VAL* 1.3 73.6 - - - +
188D ILE* 1.3 65.9 + - - +
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Residues in contact with ILE 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D GLY 3.9 14.1 - - - +
96D LEU* 4.3 14.4 - - + +
98D ALA* 3.7 31.6 - - + +
101D GLN* 4.5 0.9 - - + -
126D ILE* 3.7 31.6 - - + -
131D ALA* 3.7 21.3 - - + -
133D GLY 4.1 3.8 - - - +
134D CYS* 3.8 13.7 - - - -
157D MET* 4.3 1.6 - - - -
168D VAL* 3.7 3.6 - - - -
169D ASP* 3.4 30.8 + - + +
186D VAL* 4.3 2.2 + - + -
187D LYS* 1.3 81.1 - - - +
189D MET* 1.3 74.3 + - - +
190D LEU* 3.8 7.3 + - + +
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Residues in contact with MET 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D ALA* 4.2 10.0 - - - +
132D LYS* 3.6 37.3 + - + -
133D GLY 3.7 7.3 + - - +
156D LEU* 3.6 41.5 - - + +
157D MET* 4.0 13.6 - - - +
158D ILE* 4.1 35.9 - - - -
167D TYR* 3.2 23.8 - - + +
168D VAL* 5.1 2.0 - - + -
188D ILE* 1.3 83.1 - - - +
190D LEU* 1.3 73.0 + - - +
191D PRO* 3.8 4.9 - - - +
204D LEU* 5.3 7.2 - - + -
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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