Contacts of the strand formed by residues 221 - 227 (chain A) in PDB entry 2V5Y
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 PHE 221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166A PRO* 3.8 21.5 - - + -
168A PHE* 4.6 7.4 - + - -
187A SER* 3.8 0.3 - - - -
188A ALA* 2.9 54.8 + - + +
190A GLY 3.9 15.5 - - - -
192A THR* 3.9 15.0 - - + -
198A LEU* 4.3 14.8 - - + -
213A ILE* 3.8 28.9 - - + -
214A LYS 3.3 14.4 - - - +
215A VAL* 4.0 17.5 - - + -
216A THR* 4.3 1.8 - - - +
217A SER 5.4 0.4 - - - +
220A ARG* 1.3 76.4 - - - +
222A ILE* 1.3 69.4 + - - +
223A ALA* 4.3 8.7 - - + -
242A ILE* 3.9 22.2 - - + -
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Residues in contact with ILE 222 (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 GLN* 3.5 39.5 - - + +
186A CYS 3.4 8.7 - - - +
187A SER* 3.8 21.1 - - - +
212A GLU 4.0 0.7 - - - +
213A ILE* 3.4 1.8 - - - -
214A LYS* 2.7 51.5 + - + +
216A THR* 5.1 8.7 - - - +
221A PHE* 1.3 83.1 - - - +
223A ALA* 1.3 64.2 + - - +
224A SER* 4.1 2.7 + - - +
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Residues in contact with ALA 223 (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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168A PHE* 5.2 1.6 - - + -
184A PHE 3.5 1.9 - - - +
186A CYS* 2.8 43.9 + - + +
198A LEU* 3.5 31.4 - - + -
210A LEU* 3.7 5.6 - - + -
212A GLU 3.4 4.7 - - - -
213A ILE* 4.2 2.9 - - + +
221A PHE* 4.3 11.0 - - + -
222A ILE* 1.3 73.3 - - - +
224A SER* 1.3 59.8 + - - +
225A PHE* 3.6 14.7 - - + -
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Residues in contact with SER 224 (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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183A THR* 4.4 11.7 - - - -
184A PHE 3.3 6.3 - - - -
185A GLN* 3.0 25.3 + - - -
210A LEU* 3.5 2.8 - - - +
211A LYS* 2.8 30.3 + - - +
212A GLU* 2.7 37.0 + - - +
214A LYS* 5.8 2.1 - - - +
222A ILE* 4.4 2.9 + - - +
223A ALA* 1.3 71.1 - - - +
225A PHE* 1.3 66.3 + - - +
226A ASN* 5.2 0.4 - - - -
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Residues in contact with PHE 225 (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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168A PHE* 5.7 1.1 - + - -
182A ALA 3.9 0.2 - - - +
183A THR* 3.3 1.2 - - - -
184A PHE* 2.6 45.1 + - + +
186A CYS* 3.4 34.5 - - + -
198A LEU* 4.1 6.5 - - + -
199A TRP* 3.3 43.7 - - - -
200A LEU* 3.8 27.4 - - + -
208A ALA* 5.1 0.9 - - + -
209A PRO 3.4 21.1 - - - +
210A LEU* 3.5 30.3 - - + -
211A LYS 4.3 0.4 - - - +
223A ALA* 3.6 20.6 - - + -
224A SER* 1.3 74.4 - - - +
226A ASN* 1.3 64.8 + - - +
227A VAL 4.1 0.5 + - - -
240A CYS* 4.5 3.4 - - + -
241A MET 4.4 2.7 - - - -
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Residues in contact with ASN 226 (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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181A PHE* 3.6 25.0 - - + -
182A ALA 3.2 6.3 - - - +
183A THR* 2.3 36.8 + - - +
208A ALA* 3.6 14.3 - - - +
209A PRO* 4.3 9.7 + - - +
211A LYS* 3.5 43.5 - - + +
224A SER* 5.2 0.7 - - - -
225A PHE* 1.3 73.7 + - - +
227A VAL* 1.3 63.9 + - - +
228A VAL* 3.8 6.9 + - + +
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Residues in contact with VAL 227 (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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181A PHE* 3.2 4.0 - - - +
182A ALA* 2.8 37.4 + - + +
184A PHE* 4.2 24.7 - - + -
200A LEU* 4.2 12.8 - - + -
206A ARG 5.8 1.3 - - - +
208A ALA* 4.3 11.0 - - + -
225A PHE 4.1 0.2 + - - -
226A ASN* 1.3 72.3 - - - +
228A VAL* 1.3 61.5 + - - +
230A THR* 3.3 25.6 - - + +
234A ASP* 4.0 16.2 - - + +
238A TYR* 4.3 13.0 - - + +
256A LEU* 4.1 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