Contacts of the strand formed by residues 140 - 149 (chain D) in PDB entry 5FL6
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 LEU 140 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88D TYR* 4.0 2.5 - - - -
91D LEU* 4.8 2.5 - - + -
121D VAL* 5.1 8.7 - - + -
122D HIS 3.2 15.7 - - - +
123D LEU* 3.8 19.1 - - + -
130D VAL* 4.4 19.5 - - + -
133D ALA* 4.1 9.6 + - + +
134D LEU* 4.0 26.9 - - + -
136D ARG 4.9 0.2 + - - -
138D GLY 4.0 6.1 - - - -
139D GLY* 1.3 83.9 - - - +
141D ALA* 1.3 62.4 + - - +
142D VAL* 5.7 0.4 - - + -
199D LEU* 3.9 26.7 - - + -
205D ALA* 6.0 0.2 - - + -
207D GLY 4.5 2.2 + - - -
208D VAL* 3.5 22.1 - - + +
209D ILE* 3.0 22.3 + - - +
266D Y0R 5.9 2.2 - - - +
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Residues in contact with ALA 141 (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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80D MET* 4.1 15.7 - - + -
82D LEU* 4.3 11.2 - - + -
88D TYR* 3.5 29.3 - - + -
122D HIS* 2.8 42.6 + - - -
140D LEU* 1.3 76.3 - - - +
142D VAL* 1.3 62.2 + - - +
209D ILE* 3.2 12.1 - - + +
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Residues in contact with VAL 142 (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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119D HIS* 3.7 25.1 - - + -
120D VAL 3.4 8.3 - - - +
121D VAL* 4.3 15.3 - - + -
140D LEU* 5.7 0.7 - - + -
141D ALA* 1.3 77.7 - - - +
143D LEU* 1.3 69.1 + - - +
199D LEU* 5.2 3.4 - - + -
208D VAL* 3.9 19.5 - - + -
209D ILE 2.9 7.3 + - - +
210D TRP* 3.2 43.1 - - + -
211D THR* 3.0 28.4 + - - +
266D Y0R 4.2 9.6 - - - +
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Residues in contact with LEU 143 (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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48D LEU* 3.9 22.0 - - + -
50D LEU* 4.4 11.9 - - + -
53D PHE* 5.7 0.7 - - + -
80D MET* 4.1 30.3 - - + -
82D LEU* 4.4 1.6 - - + -
118D ILE 3.6 0.9 - - - +
119D HIS* 3.3 5.5 - - - -
120D VAL* 2.8 44.4 + - + +
122D HIS* 3.7 23.1 - - + +
141D ALA* 6.0 0.2 - - + -
142D VAL* 1.3 74.5 - - - +
144D ALA* 1.3 58.8 + - - +
185D LEU* 4.2 21.7 - - + +
211D THR* 3.6 19.1 - - + +
213D PHE* 4.2 16.6 - - + -
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Residues in contact with ALA 144 (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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117D GLU* 3.8 13.2 - - - +
118D ILE 3.2 4.5 - - - -
119D HIS* 3.7 20.9 - - + -
143D LEU* 1.3 73.9 - - - +
145D ALA* 1.3 60.3 + - - +
210D TRP* 4.2 10.1 - - + -
211D THR 2.8 14.6 + - - +
212D VAL* 3.4 18.5 - - + +
213D PHE* 3.0 32.4 + - - -
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Residues in contact with ALA 145 (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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117D GLU* 3.3 8.0 - - - +
118D ILE* 2.9 48.8 + - + +
144D ALA* 1.3 76.1 - - - +
146D PHE* 1.3 68.3 + - - +
185D LEU* 4.4 2.5 - - + -
186D PRO* 3.7 35.2 - - + -
212D VAL* 5.6 0.7 - - - -
213D PHE* 4.0 8.3 - - + +
215D GLN 4.9 0.4 - - - +
217D VAL* 4.6 3.6 - - + -
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Residues in contact with PHE 146 (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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34D ILE* 4.6 0.7 - - + -
105D SER* 4.0 7.4 - - - -
107D HIS* 3.4 40.4 - - + -
109D VAL* 3.8 18.8 - - + -
114D PHE* 3.4 56.3 - + + -
116D ALA 3.7 2.2 - - - -
117D GLU* 3.7 17.0 - - + -
145D ALA* 1.3 73.4 - - - +
147D LEU* 1.3 63.9 + - - +
193D PHE* 6.3 1.1 - + - -
212D VAL* 3.8 22.4 - - + -
213D PHE 4.3 11.9 + - - -
214D ASN 5.3 1.3 - - - -
215D GLN 5.1 0.6 + - - -
216D THR* 3.5 22.1 - - + +
217D VAL* 3.0 24.8 + - - +
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Residues in contact with LEU 147 (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 LEU* 4.4 13.5 - - + -
114D PHE* 4.2 0.7 - - - +
115D PRO* 3.2 22.2 - - - +
116D ALA* 2.9 42.7 + - + +
117D GLU* 4.2 4.0 - - - +
118D ILE* 4.1 11.9 - - + -
145D ALA 4.2 0.2 - - - +
146D PHE* 1.3 80.2 - - - +
148D GLU* 1.3 61.8 + - - +
157D TYR* 3.4 42.0 - - + +
217D VAL* 3.3 21.3 - - + +
219D LEU* 4.0 22.7 - - + -
224D LEU* 4.6 5.6 - - + -
227D LEU* 4.6 4.9 - - + -
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Residues in contact with GLU 148 (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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112D HIS* 4.8 5.4 + - - -
114D PHE* 3.4 30.6 - - + -
115D PRO* 4.0 9.7 - - + +
147D LEU* 1.3 76.7 - - - +
149D GLU* 1.3 64.7 + - - +
216D THR* 2.7 36.3 + - - +
217D VAL 2.8 8.9 + - - +
218D MET* 3.4 20.4 - - - +
219D LEU* 2.8 26.7 + - - +
224D LEU* 4.0 5.9 - - - +
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Residues in contact with GLU 149 (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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115D PRO* 4.2 7.1 - - + +
148D GLU* 1.3 74.9 - - - +
150D GLY* 1.3 64.0 + - - +
218D MET* 3.9 7.4 - - - +
219D LEU 3.4 3.4 - - - -
221D ALA* 3.8 40.3 - - - +
224D LEU* 3.7 14.3 - - + +
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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