Contacts of the strand formed by residues 179 - 186 (chain A) in PDB entry 3F00
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 PRO 179 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A LEU* 3.6 20.4 - - + -
177A SER* 3.2 7.4 - - - +
178A ASP* 1.3 85.1 - - - +
180A TYR* 1.3 59.3 + - - +
198A HIS 2.9 41.7 + - - +
201A THR 3.2 26.7 - - - +
204A PRO* 3.6 27.4 - - + -
206A PHE* 3.8 7.0 - - + -
228A VAL* 4.1 9.2 - - + -
229A TYR 3.2 10.1 - - - +
230A ASP* 4.7 0.9 - - - -
240A ILE* 4.6 2.5 - - + -
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Residues in contact with TYR 180 (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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179A PRO* 1.3 75.7 - - - +
181A VAL* 1.3 71.5 + - - +
182A LYS* 3.8 23.6 + - + -
194A GLU* 3.6 35.4 + - - -
195A THR* 3.4 18.8 - - - +
196A LYS 3.6 8.7 - - - +
197A VAL* 3.9 22.0 - - + -
206A PHE* 4.0 2.9 - - - -
228A VAL* 3.4 4.4 - - - +
229A TYR* 2.9 59.2 + - + +
231A PHE* 3.9 20.2 - + + -
237A HIS* 2.6 38.5 + + - +
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Residues in contact with VAL 181 (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 LEU* 4.1 25.1 - - + -
162A ILE* 3.8 13.2 - - + -
180A TYR* 1.3 79.5 - - - +
182A LYS* 1.3 75.5 + - - +
183A VAL* 4.0 12.8 + - + +
194A GLU* 3.2 4.2 - - - +
195A THR* 2.9 43.4 + - + +
206A PHE* 3.7 29.6 - - + -
226A MET* 4.3 2.2 - - + -
227A ALA 3.3 16.8 - - - +
228A VAL* 4.2 7.0 - - + -
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Residues in contact with LYS 182 (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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180A TYR* 3.8 19.2 + - + -
181A VAL* 1.3 73.4 - - - +
183A VAL* 1.3 61.8 + - - +
184A PHE* 4.1 15.8 - - + -
192A LYS* 3.9 26.1 - - + +
193A PHE 3.3 6.7 - - - +
194A GLU* 3.4 32.3 + - + +
225A VAL 3.6 0.7 - - - +
226A MET* 3.4 4.7 - - - -
227A ALA* 2.8 35.2 + - + +
229A TYR* 3.4 42.0 + - + +
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Residues in contact with VAL 183 (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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160A VAL* 4.2 15.5 - - + -
162A ILE* 3.7 30.5 - - + -
181A VAL* 4.0 11.7 - - + +
182A LYS* 1.3 80.5 - - - +
184A PHE* 1.3 64.9 + - - +
193A PHE* 2.8 43.4 + - + +
210A PHE* 4.2 14.6 - - + -
212A PHE* 4.0 14.1 - - + -
224A LEU* 3.9 21.1 - - + -
225A VAL 3.4 6.1 - - - +
226A MET* 4.2 4.7 - - + -
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Residues in contact with PHE 184 (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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182A LYS* 4.3 13.5 - - + -
183A VAL* 1.3 87.6 - - - +
185A LEU* 1.3 67.1 + - - +
186A LEU* 4.0 22.7 - - + -
188A ASP 5.8 0.9 - - - -
190A LYS 5.2 4.3 - - - +
191A LYS 5.3 0.2 - - - +
192A LYS* 3.3 58.8 - - + -
212A PHE* 4.0 9.6 - - - -
224A LEU* 3.5 6.3 - - - +
225A VAL* 2.9 70.4 + - + -
227A ALA* 4.9 6.1 - - + -
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Residues in contact with LEU 185 (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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158A LEU* 4.4 11.2 - - + -
184A PHE* 1.3 80.0 - - - +
186A LEU* 1.3 64.5 + - - +
188A ASP* 3.2 45.5 - - + +
212A PHE* 3.7 40.1 - - + -
214A VAL* 4.1 17.7 - - + -
219A LEU* 4.4 10.8 - - + -
222A LYS* 4.3 14.8 - - + +
223A THR 3.3 12.6 - - - +
224A LEU* 3.9 25.4 - - + +
247A MET* 4.7 5.2 - - + -
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Residues in contact with LEU 186 (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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184A PHE* 4.0 18.4 - - + -
185A LEU* 1.3 74.0 - - - +
187A PRO* 1.3 71.7 - - + +
188A ASP* 3.2 9.9 - - - +
192A LYS* 5.7 1.1 - - - +
221A GLY 5.3 0.2 - - - -
222A LYS* 3.2 9.4 - - - +
223A THR* 2.7 42.2 + - - +
225A VAL* 3.7 28.3 - - + -
244A LYS* 4.5 14.8 - - + +
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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