Contacts of the strand formed by residues 181 - 187 (chain L) in PDB entry 2FIE
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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174L VAL* 3.5 28.9 - - + -
175L LEU 3.5 2.9 - - - +
176L ALA* 3.8 14.6 - - + -
180L GLY* 1.3 75.8 - - - -
182L ASN* 1.3 67.3 + - - +
199L ASP* 3.2 11.8 + - - +
200L VAL* 2.7 52.8 + - + +
256L LEU* 4.5 5.8 - - + -
287L VAL* 3.6 29.6 - - + +
290L LYS* 3.8 9.4 + - + -
291L ALA* 3.9 11.4 - - + +
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Residues in contact with ASN 182 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16L PHE* 3.1 36.1 - - - -
174L VAL* 3.4 3.9 - - - -
175L LEU* 3.0 37.8 + - - +
179L CYS* 4.7 4.9 - - - -
180L GLY* 4.4 9.3 + - - -
181L VAL* 1.3 77.9 - - - +
183L CYS* 1.3 64.5 + - - +
184L PHE* 3.4 26.1 - - + -
195L LEU* 3.9 6.0 - - + +
197L ASP 3.4 2.7 - - - -
198L LYS* 3.5 12.3 - - - +
199L ASP* 2.9 28.4 + - - +
200L VAL* 4.8 0.2 - - - -
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Residues in contact with CYS 183 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172L MET* 3.7 20.9 - - - -
173L LEU 3.6 3.4 - - - -
174L VAL* 3.8 25.8 - - - -
181L VAL* 5.0 0.7 - - - -
182L ASN* 1.3 72.5 - - - +
184L PHE* 1.3 63.2 + - - +
195L LEU* 3.1 6.8 - - - +
196L VAL* 2.9 29.1 + - + -
197L ASP* 3.0 24.3 + - + -
200L VAL* 3.9 20.4 - - - -
253L HIS* 4.7 6.5 - - - -
256L LEU* 5.2 4.3 - - - -
257L VAL* 6.1 1.6 - - - -
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Residues in contact with PHE 184 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12L THR 4.0 1.3 - - - -
13L LEU* 3.6 51.8 - - + -
16L PHE* 3.8 28.0 - + + -
172L MET* 3.3 8.2 - - - +
173L LEU* 2.9 42.5 + - + +
175L LEU* 4.3 10.1 - - + -
182L ASN* 3.4 39.7 - - + -
183L CYS* 1.3 76.9 - - - +
185L MET* 1.3 60.4 + - - +
193L PHE* 3.9 21.5 - - + -
194L ILE 3.0 6.3 - - - +
195L LEU* 3.8 29.8 - - + -
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Residues in contact with MET 185 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50H LYS* 3.5 48.0 - - + +
53H ILE* 3.6 15.8 - - + +
129H LEU* 4.3 9.2 - - + -
170L ALA* 3.9 22.9 - - + -
171L THR 3.9 2.5 - - - +
172L MET* 3.3 30.7 - - + -
184L PHE* 1.3 74.5 - - - +
186L LEU* 1.3 64.4 + - - +
187L ASP 3.5 1.9 + - - -
193L PHE* 3.3 2.5 - - - -
194L ILE* 2.7 39.6 + - - +
196L VAL* 3.7 24.5 - - + +
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Residues in contact with LEU 186 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49H ARG 3.7 6.8 - - - +
50H LYS* 4.0 4.9 - - - +
53H ILE* 4.8 0.2 - - - -
42L LYS* 4.1 22.4 - - + +
45L SER* 4.0 16.2 - - - +
171L THR* 2.9 49.2 + - + +
185L MET* 1.3 71.4 - - - +
187L ASP* 1.3 56.1 + - - +
188L PRO* 2.7 35.0 - - + +
191L GLY* 4.2 4.3 - - - -
192L GLU 3.5 28.9 - - - +
193L PHE* 3.6 21.7 - - + -
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Residues in contact with ASP 187 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50H LYS 3.8 3.1 - - - -
51H ALA 2.3 24.2 - - - +
52H GLY* 2.9 6.6 - - - -
53H ILE* 2.8 19.7 + - + -
54H ALA* 2.7 33.2 + - - +
55H HIS* 5.4 0.5 - - - -
185L MET 3.5 2.6 + - - -
186L LEU* 1.3 69.1 - - - +
188L PRO* 1.3 66.7 - - - +
189L ALA* 2.9 18.5 + - - +
190L ILE* 3.1 11.4 + - + +
191L GLY* 3.0 17.8 + - - -
192L GLU 2.9 14.6 + - - +
194L ILE* 3.7 14.4 - - + -
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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