Contacts of the strand formed by residues 140 - 149 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88B TYR* 4.2 2.5 - - - -
91B LEU* 4.9 2.9 - - + -
121B VAL* 5.1 12.6 - - + -
122B HIS 3.3 15.5 - - - +
123B LEU* 3.7 21.3 - - + -
130B VAL* 4.5 18.2 - - + -
133B ALA* 4.1 11.5 + - + +
134B LEU* 3.7 30.1 - - + -
136B ARG 4.8 0.2 + - - -
138B GLY 3.9 5.9 - - - -
139B GLY* 1.3 81.5 - - - +
141B ALA* 1.3 62.1 + - - +
142B VAL* 5.5 0.4 - - + -
199B LEU* 4.1 18.6 - - + -
207B GLY 4.6 2.4 + - - -
208B VAL* 3.5 20.8 - - + -
209B ILE* 3.0 23.1 + - - +
269B Y0R 5.5 3.6 - - - +
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Residues in contact with ALA 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B MET* 4.1 15.7 - - + -
82B LEU* 4.1 11.7 - - + -
88B TYR* 3.6 30.4 - - + -
122B HIS* 2.8 42.6 + - - +
140B LEU* 1.3 75.8 - - - +
142B VAL* 1.3 62.2 + - - +
209B ILE* 3.2 12.6 - - + +
211B THR* 6.1 0.4 - - - +
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Residues in contact with VAL 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B HIS* 3.7 24.7 - - + -
120B VAL 3.3 9.0 - - - +
121B VAL* 4.3 16.2 - - + -
140B LEU* 5.5 0.9 - - + -
141B ALA* 1.3 78.3 - - - +
143B LEU* 1.3 68.3 + - - +
199B LEU* 5.5 1.6 - - + -
208B VAL* 3.8 20.4 - - + -
209B ILE 2.9 7.5 + - - +
210B TRP* 3.3 37.0 - - + -
211B THR* 3.0 28.4 + - - +
269B Y0R 4.1 15.3 - - - +
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Residues in contact with LEU 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B LEU* 4.2 18.2 - - + -
50B LEU* 3.9 36.6 - - + -
80B MET* 4.1 19.7 - - + -
82B LEU* 4.5 4.0 - - + -
118B ILE 3.6 1.4 - - - +
119B HIS* 3.4 3.3 - - - -
120B VAL* 2.9 44.6 + - + +
122B HIS* 3.7 23.6 - - + -
141B ALA* 6.0 0.2 - - + -
142B VAL* 1.3 73.3 - - - +
144B ALA* 1.3 59.5 + - - +
185B LEU* 4.7 9.1 - - + +
211B THR* 3.5 25.8 - - + +
213B PHE* 4.3 11.4 - - + -
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Residues in contact with ALA 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B GLU* 3.7 13.0 - - - +
118B ILE 3.2 4.5 - - - -
119B HIS* 3.7 21.5 - - + +
142B VAL 3.9 0.2 + - - -
143B LEU* 1.3 73.7 - - - +
145B ALA* 1.3 61.3 + - - +
185B LEU* 5.9 0.2 - - - -
210B TRP* 4.2 9.9 - - + -
211B THR 2.8 15.2 + - - +
212B VAL* 3.4 19.3 - - + +
213B PHE* 3.0 32.1 + - - -
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Residues in contact with ALA 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B GLU* 3.3 6.8 - - - +
118B ILE* 2.9 49.0 + - + +
144B ALA* 1.3 75.6 - - - +
146B PHE* 1.3 67.8 + - - +
147B LEU 3.8 0.2 + - - -
185B LEU* 4.6 4.3 - - + -
186B PRO* 3.8 35.4 - - + -
212B VAL* 5.4 0.4 - - - -
213B PHE* 4.0 7.4 - - + -
217B VAL* 5.1 4.0 - - + -
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Residues in contact with PHE 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ILE* 4.6 1.1 - - + -
105B SER* 4.0 3.8 - - - -
107B HIS* 3.3 42.0 - - + -
109B VAL* 3.7 19.1 - - + -
114B PHE* 3.3 53.8 - + + -
116B ALA 3.6 2.2 - - - -
117B GLU* 3.5 21.1 - - - -
145B ALA* 1.3 74.6 - - - +
147B LEU* 1.3 59.9 + - - +
148B GLU 4.1 0.4 - - - -
193B PHE* 6.3 0.9 - + - -
212B VAL* 3.8 21.3 - - + -
213B PHE 4.4 11.0 + - - -
214B ASN 5.2 3.1 - - - -
215B GLN 5.0 1.4 + - - -
216B THR* 3.5 22.1 - - + +
217B VAL* 3.0 28.2 + - - +
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Residues in contact with LEU 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B LEU* 4.2 12.8 - - + -
114B PHE* 4.1 0.7 - - - +
115B PRO* 3.3 11.7 - - - +
116B ALA* 2.9 53.8 + - + +
117B GLU* 4.1 2.2 - - - +
118B ILE* 4.0 13.7 - - + -
145B ALA 4.0 0.4 - - - +
146B PHE* 1.3 74.9 - - - +
148B GLU* 1.3 61.0 + - - +
157B TYR* 3.3 36.1 - - + +
217B VAL* 3.2 30.1 - - + -
219B LEU* 3.8 28.0 - - + -
224B LEU* 4.8 2.7 - - + -
227B LEU* 4.6 4.9 - - + -
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Residues in contact with GLU 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B HIS* 4.7 5.2 + - - -
114B PHE* 3.6 32.3 - - + -
115B PRO* 4.0 8.8 - - + +
147B LEU* 1.3 74.3 - - - +
149B GLU* 1.3 62.4 + - - +
216B THR* 2.7 37.2 + - + +
217B VAL 2.8 10.6 + - - +
218B MET* 3.2 9.9 - - + +
219B LEU* 2.8 32.4 + - - +
224B LEU* 4.1 5.8 - - - -
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Residues in contact with GLU 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B PRO* 4.2 7.8 - - + +
148B GLU* 1.3 76.2 - - - +
150B GLY* 1.3 64.5 + - - +
218B MET* 4.3 6.8 - - - +
219B LEU 3.3 4.0 - - - -
221B ALA* 3.8 40.4 - - - +
224B LEU* 3.8 12.7 - - + +
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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