Contacts of the strand formed by residues 144 - 149 (chain A) in PDB entry 2FPL
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 LYS 144 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A LEU* 3.5 5.9 - - - +
142A GLN* 3.7 12.6 - - - +
143A PRO* 1.3 78.6 - - - +
145A ALA* 1.3 60.9 + - - +
175A ASP 4.2 4.9 + - - -
176A ASN* 2.5 50.5 - - - +
178A PHE* 3.8 15.7 - - + -
202A GLY 5.4 1.3 - - - -
203A ASN* 3.3 39.9 - - + +
204A ASN 2.8 14.1 + - - +
205A ILE* 3.6 14.5 - - + -
206A LYS 2.8 23.9 + - - -
207A LEU 3.3 5.0 + - - -
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Residues in contact with ALA 145 (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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119A CYS* 4.1 9.6 - - + +
122A LEU* 4.0 6.9 - - + +
123A GLN* 5.8 0.2 - - - +
144A LYS* 1.3 75.4 - - - +
146A VAL* 1.3 59.5 + - - +
176A ASN 2.9 8.0 + - - +
177A THR* 3.3 22.3 - - + +
178A PHE* 2.6 37.9 + - - -
207A LEU* 3.3 31.6 - - + +
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Residues in contact with VAL 146 (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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145A ALA* 1.3 79.3 - - - +
147A TYR* 1.3 58.9 + - - +
148A ILE* 4.2 16.4 - - + -
178A PHE* 3.3 9.0 - - + +
180A ALA* 5.9 3.4 - - + -
191A PHE 5.7 0.4 - - - +
195A ILE* 3.9 26.2 - - + -
198A LEU* 3.8 20.2 - - + -
205A ILE* 3.7 34.1 - - + -
207A LEU 2.7 12.3 + - - +
208A VAL* 3.3 8.8 - - + -
209A VAL* 2.7 34.3 + - - +
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Residues in contact with TYR 147 (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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112A THR* 3.6 1.9 - - - +
115A MET* 3.8 23.8 - - + +
116A HIS* 3.2 31.5 + + - -
119A CYS* 3.7 20.0 - - - -
146A VAL* 1.3 74.9 - - - +
148A ILE* 1.3 62.9 + - - +
149A ASP* 3.4 34.0 + - + -
153A THR 5.1 0.2 - - - -
154A PHE* 3.8 28.7 + + + -
177A THR* 4.3 6.7 - - + -
178A PHE 2.6 14.3 + - - +
179A VAL* 3.3 13.3 - - + +
180A ALA 2.9 25.8 + - - -
209A VAL* 3.8 15.5 - - + -
211A ASP* 3.2 28.6 + - + -
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Residues in contact with ILE 148 (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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146A VAL* 4.2 13.0 - - + -
147A TYR* 1.3 74.4 - - - +
149A ASP* 1.3 60.8 + - - +
150A THR* 3.7 2.1 + - - +
180A ALA* 3.5 11.7 - - + +
182A ALA* 4.4 18.8 - - + -
188A GLN* 4.0 18.4 - - + +
191A PHE* 3.8 16.4 - - + +
192A ALA* 3.6 32.3 - - - +
195A ILE* 4.6 8.1 - - + -
208A VAL* 5.3 0.2 - - + -
209A VAL 2.8 17.3 + - - +
210A ILE* 3.5 28.2 - - + +
211A ASP 3.0 27.9 + - - +
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Residues in contact with ASP 149 (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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147A TYR* 3.4 19.7 + - + -
148A ILE* 1.3 71.5 - - - +
150A THR* 1.3 57.7 + - - +
151A GLU* 3.2 5.4 + - - -
152A GLY* 2.8 41.4 + - - -
153A THR* 3.1 16.4 + - - -
154A PHE* 3.3 19.8 + - + +
179A VAL* 4.6 6.0 - - + +
180A ALA 2.9 11.5 + - - +
181A ARG* 3.2 15.9 + - - -
182A ALA* 2.8 25.5 + - - -
211A ASP* 3.3 7.3 - - - +
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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