Contacts of the strand formed by residues 211 - 218 (chain A) in PDB entry 2FIN
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 211 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A ILE* 3.5 34.3 - - + -
174A VAL* 3.4 4.3 - - - +
175A SER* 3.1 22.4 - - - +
176A TYR 5.4 0.2 - - - -
177A GLU* 3.8 26.7 - - + +
179A ILE* 4.3 6.1 - - + -
198A ARG* 3.2 24.1 - - - +
199A ILE* 3.6 18.6 + - + +
208A GLU 4.2 10.8 - - - +
209A LEU 4.7 0.9 - - - -
210A GLU* 1.3 81.8 - - - +
212A LYS* 1.3 68.0 + - - +
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Residues in contact with LYS 212 (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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171A HIS 4.8 1.3 - - - -
172A LYS 3.8 17.7 - - - -
173A LYS* 4.5 3.8 - - - +
174A VAL* 3.6 22.9 - - + +
175A SER 2.8 16.0 + - - +
176A TYR* 3.4 8.6 - - + +
177A GLU 3.1 21.7 + - - -
196A SER* 6.1 0.2 - - - -
197A VAL 3.2 17.0 - - - +
198A ARG* 4.2 5.8 - - + +
211A VAL* 1.3 80.3 - - - +
213A ASP* 1.3 80.6 + - - +
214A GLY* 5.6 1.4 - - - -
225A GLY 4.6 1.2 + - - -
226A ALA* 3.3 21.5 - - + +
227A THR 3.1 38.2 + - - +
229A ASP* 3.6 13.9 + - - -
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Residues in contact with ASP 213 (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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176A TYR* 6.1 0.4 - - - -
177A GLU 3.3 18.2 - - - +
178A ASP* 5.1 1.1 - - - -
179A ILE* 3.0 36.7 - - - +
180A ILE* 3.2 31.8 + - + +
196A SER* 3.4 5.0 - - - -
197A VAL* 3.0 37.0 + - - +
212A LYS* 1.3 93.6 + - - +
214A GLY* 1.3 60.0 + - - +
215A PHE* 5.4 4.0 - - + -
226A ALA* 6.4 0.2 - - - -
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Residues in contact with GLY 214 (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 ILE* 3.7 10.3 - - - +
195A PHE 2.8 18.2 - - - -
196A SER* 4.2 0.7 - - - -
212A LYS* 5.6 1.8 - - - -
213A ASP* 1.3 79.4 - - - +
215A PHE* 1.3 71.6 + - - -
216A LYS* 5.6 0.2 - - - -
224A LYS* 4.1 1.7 - - - +
225A GLY 3.8 24.7 + - - +
226A ALA* 5.6 0.5 - - - +
229A ASP* 5.6 1.6 - - - -
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Residues in contact with PHE 215 (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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178A ASP* 6.1 0.9 - - - -
180A ILE* 4.2 30.5 - - + -
183A THR* 6.2 0.9 - - + -
194A GLU* 4.0 2.6 - - - +
195A PHE* 3.2 45.5 + + + +
213A ASP* 5.4 3.8 - - + -
214A GLY* 1.3 86.3 - - - -
216A LYS* 1.3 72.2 + - - +
222A ALA* 5.7 5.8 - - + -
223A SER* 3.6 10.3 - - - +
224A LYS* 3.6 40.6 - - + -
13B PHE* 5.5 10.3 - - + -
14B SER* 5.4 10.8 - - - -
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Residues in contact with LYS 216 (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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193A LEU 4.7 0.7 - - - -
194A GLU* 4.8 19.5 - - + +
195A PHE* 4.5 0.9 - - - -
214A GLY 5.6 0.2 - - - -
215A PHE* 1.3 83.0 - - - +
217A TYR* 1.3 54.8 + - - +
218A VAL* 3.9 10.7 - - + +
221A SER 2.8 22.2 - - - +
222A ALA* 3.6 1.3 - - - -
223A SER* 3.0 39.1 + - - +
224A LYS 5.6 0.4 - - - -
225A GLY* 5.0 19.0 + - - +
227A THR* 4.9 18.9 - - - +
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Residues in contact with TYR 217 (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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185A VAL* 4.2 17.5 - - + +
187A THR* 2.9 33.2 + - + +
190A VAL 4.1 2.7 - - - -
191A LYS 3.3 23.6 - - - -
192A ASN* 3.1 7.2 - - - +
193A LEU* 2.9 60.0 + - + +
194A GLU* 4.7 2.0 - - - +
195A PHE* 3.9 12.1 - + + -
216A LYS* 1.3 70.2 - - - +
218A VAL* 1.3 65.0 + - - +
220A GLY* 3.3 36.9 - - - -
221A SER 3.3 2.9 - - - -
222A ALA* 4.4 8.5 - - + +
9B THR* 4.9 8.1 + - - +
13B PHE* 3.7 34.0 - + - -
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Residues in contact with VAL 218 (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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191A LYS* 4.1 7.2 - - - +
192A ASN* 3.3 25.4 - - + +
194A GLU* 5.8 5.2 - - + +
216A LYS* 4.4 9.9 - - + +
217A TYR* 1.3 83.1 - - - +
219A ASP* 1.3 71.7 + - + +
220A GLY 3.3 0.4 - - - -
221A SER* 2.8 34.1 + - - +
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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