Contacts of the strand formed by residues 140 - 149 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88C TYR* 4.1 2.0 - - - -
91C LEU* 5.1 2.2 - - + -
121C VAL* 5.1 11.4 - - + -
122C HIS 3.3 14.6 - - - +
123C LEU* 3.9 12.3 - - + -
130C VAL* 4.4 17.3 - - + -
133C ALA* 3.9 21.2 + - + +
134C LEU* 3.9 27.6 - - + -
136C ARG 4.7 0.2 + - - -
138C GLY 4.0 5.7 - - - -
139C GLY* 1.3 82.4 - - - +
141C ALA* 1.3 62.1 + - - +
142C VAL* 5.5 0.9 - - + -
199C LEU* 3.9 21.5 - - + -
207C GLY 4.7 2.0 + - - -
208C VAL* 3.5 21.2 - - + +
209C ILE* 3.0 22.7 + - - +
267C Y0R 5.4 3.4 - - - +
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Residues in contact with ALA 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C MET* 4.1 15.3 - - + -
82C LEU* 4.1 11.4 - - + -
88C TYR* 3.5 31.2 - - + -
122C HIS* 2.9 37.1 + - - -
140C LEU* 1.3 75.5 - - - +
142C VAL* 1.3 64.8 + - - +
143C LEU* 6.0 0.4 - - + -
209C ILE* 3.2 11.7 - - + +
211C THR* 6.1 0.2 - - - +
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Residues in contact with VAL 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C HIS* 3.7 23.8 - - + -
120C VAL 3.4 10.8 - - - +
121C VAL* 4.2 15.3 - - + -
140C LEU* 5.4 1.3 - - + -
141C ALA* 1.3 78.3 - - - +
143C LEU* 1.3 66.9 + - - +
144C ALA 3.9 0.2 + - - -
199C LEU* 5.7 2.2 - - + -
208C VAL* 3.8 20.2 - - + -
209C ILE 2.9 7.4 + - - +
210C TRP* 3.4 40.0 - - + -
211C THR* 3.0 28.8 + - - +
267C Y0R 4.2 11.9 - - - +
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Residues in contact with LEU 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C LEU* 4.0 18.4 - - + -
50C LEU* 4.0 35.4 - - + -
80C MET* 4.2 18.8 - - + -
82C LEU* 4.7 2.5 - - + -
118C ILE* 3.6 1.2 - - - +
119C HIS* 3.4 3.6 - - - -
120C VAL* 2.9 43.1 + - + +
122C HIS* 3.8 25.6 - - + +
141C ALA* 4.2 0.6 - - + -
142C VAL* 1.3 74.7 - - - +
144C ALA* 1.3 60.5 + - - +
185C LEU* 4.6 10.2 - - + +
211C THR* 3.5 26.2 - - + +
213C PHE* 4.3 11.7 - - + -
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Residues in contact with ALA 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C GLU* 3.7 12.8 - - - +
118C ILE 3.3 5.2 - - - -
119C HIS* 3.7 20.4 - - + +
143C LEU* 1.3 74.7 - - - +
145C ALA* 1.3 59.9 + - - +
210C TRP* 4.1 9.4 - - + -
211C THR 2.8 14.0 + - - +
212C VAL* 3.3 19.6 - - + +
213C PHE* 2.9 32.7 + - - -
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Residues in contact with ALA 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C GLU* 3.4 6.8 - - - +
118C ILE* 2.9 48.8 + - + +
144C ALA* 1.3 75.8 - - - +
146C PHE* 1.3 67.1 + - - +
147C LEU* 5.2 0.4 - - + -
185C LEU* 4.6 3.1 - - + +
186C PRO* 3.8 35.0 - - + -
212C VAL* 5.5 0.7 - - - -
213C PHE* 4.0 8.1 - - + +
217C VAL* 5.0 4.3 - - + -
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Residues in contact with PHE 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C ILE* 4.7 1.3 - - + -
105C SER* 4.0 3.4 - - - -
107C HIS* 3.4 40.2 - - + -
109C VAL* 3.7 26.5 - - + -
114C PHE* 3.3 45.8 - + + -
116C ALA 3.6 2.2 - - - -
117C GLU* 3.6 21.3 - - - -
145C ALA* 1.3 74.6 - - - +
147C LEU* 1.3 63.2 + - - +
193C PHE* 6.1 1.6 - + - -
212C VAL* 3.9 20.6 - - + -
213C PHE 4.4 11.0 + - - -
214C ASN 5.2 2.7 - - - -
215C GLN 5.0 1.0 + - - -
216C THR* 3.5 22.2 - - + +
217C VAL* 3.0 24.9 + - - +
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Residues in contact with LEU 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C LEU* 4.2 13.7 - - + -
114C PHE* 4.1 1.0 - - - +
115C PRO* 3.4 13.4 - - - +
116C ALA* 2.9 55.5 + - + +
117C GLU* 4.1 2.5 - - - +
118C ILE* 4.1 13.0 - - + +
145C ALA 4.1 0.7 - - - +
146C PHE* 1.3 79.3 - - - +
148C GLU* 1.3 59.7 + - - +
157C TYR* 3.4 45.3 - - + +
217C VAL* 3.4 16.2 - - + +
219C LEU* 4.0 23.3 - - + -
224C LEU* 4.7 4.3 - - + -
227C LEU* 4.6 4.7 - - + -
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Residues in contact with GLU 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C HIS* 5.0 3.3 + - - -
114C PHE* 3.6 33.9 - - + -
115C PRO* 4.1 8.7 - - + -
147C LEU* 1.3 75.0 - - - +
149C GLU* 1.3 66.7 + - - +
216C THR* 2.7 35.5 + - - +
217C VAL 2.9 10.9 + - - +
218C MET* 3.3 9.2 - - + +
219C LEU* 2.8 27.7 + - - +
224C LEU* 4.2 5.3 - - - +
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Residues in contact with GLU 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C PRO* 4.3 6.9 - - + +
148C GLU* 1.3 78.5 - - - +
150C GLY* 1.3 64.4 + - - +
218C MET* 4.3 5.2 - - - +
219C LEU 3.2 3.8 - - - +
220C SER 4.2 0.4 - - - -
221C ALA* 3.7 41.4 - - - +
224C LEU* 3.9 14.5 - - + +
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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