Contacts of the strand formed by residues 223 - 228 (chain A) in PDB entry 5V8V
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 223 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A PHE* 3.4 13.4 - - - -
221A GLU* 2.7 17.2 + - + +
222A ASP* 1.3 81.3 - - - +
224A PHE* 1.3 56.2 + - - +
245A GLY* 2.8 50.7 + - - +
246A GLY* 3.6 15.3 - - - -
392A GLU* 4.3 19.7 - - + +
393A PHE 3.3 9.9 - - - +
394A ASP* 3.4 36.3 - - + +
396A ARG* 5.8 0.2 - - + -
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Residues in contact with PHE 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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105A THR* 3.9 6.5 - - + -
196A MET* 3.5 46.4 - - + -
210A PHE* 3.6 33.7 - + + -
223A VAL* 1.3 75.8 - - - +
225A SER* 1.3 57.3 + - - +
226A PHE* 3.7 21.1 - + - -
242A ILE* 4.5 1.8 - - + -
243A VAL 3.1 14.8 - - - +
244A LEU* 4.0 16.4 - - + -
245A GLY 4.4 0.4 - - - +
246A GLY 4.3 2.2 - - - -
267A TRP* 3.8 22.4 - + - -
392A GLU* 3.7 0.6 - - - +
393A PHE* 2.7 66.5 + + + +
395A ARG* 4.8 1.1 - - + -
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Residues in contact with SER 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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224A PHE* 1.3 76.9 - - - +
226A PHE* 1.3 66.4 + - - +
242A ILE* 3.1 9.7 - - - +
243A VAL* 2.9 33.4 + - - +
246A GLY 2.8 18.7 + - - -
247A SER* 3.4 19.6 + - - -
390A TYR* 2.8 27.5 + - - -
391A THR 3.2 13.7 - - - -
392A GLU* 3.8 4.3 - - - -
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Residues in contact with PHE 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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78A LEU* 4.8 3.6 - - + -
103A PHE* 3.6 39.3 - - + -
105A THR* 4.1 2.0 - - + -
196A MET* 4.7 2.0 - - + -
224A PHE* 3.7 28.3 - + - -
225A SER* 1.3 79.1 - - - +
227A TYR* 1.3 59.7 + - - +
228A TYR* 3.5 37.7 - + + -
241A GLN 3.6 2.7 - - - -
242A ILE* 3.7 19.3 - - + -
293A THR* 3.6 22.4 - - + -
386A ILE* 4.4 15.3 - - + +
390A TYR* 3.4 13.4 - - - -
391A THR* 2.8 29.6 + - - +
393A PHE* 3.5 19.5 - + + -
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Residues in contact with TYR 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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226A PHE* 1.3 73.6 - - - +
228A TYR* 1.3 75.4 + - - +
229A ASN* 3.1 44.2 + - + -
230A ARG* 5.8 1.9 + - - -
238A LEU* 4.3 12.3 - - + -
240A GLY* 3.2 7.9 - - - -
241A GLN* 2.8 51.7 + - + +
251A HIS* 3.6 45.9 + + + +
386A ILE* 5.3 1.1 - - - -
387A ARG 5.6 0.2 - - - -
390A TYR* 3.5 24.5 - + + +
405A ALA* 4.5 14.1 - - + -
406A ARG* 3.6 25.6 + - - -
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Residues in contact with TYR 228 (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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78A LEU* 3.6 24.6 - - + +
86A TYR* 3.5 43.0 + + + +
102A VAL* 5.5 0.3 - - - +
103A PHE 4.0 2.9 + - - -
226A PHE* 3.5 31.0 - + + -
227A TYR* 1.3 87.1 - - - +
229A ASN* 1.3 62.8 + - - +
239A GLY 4.3 0.2 - - - -
293A THR* 2.8 28.8 + - - -
383A ALA* 3.9 25.1 - - + -
386A ILE* 4.2 26.3 + - + +
387A ARG* 3.4 36.9 - - + +
503A 90D 3.7 12.1 - - - -
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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