Contacts of the strand formed by residues 250 - 255 (chain A) in PDB entry 2AY6
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 250 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218A LEU* 4.1 0.9 - - - +
219A PRO* 3.8 16.4 - - + +
221A ILE* 4.0 26.5 - - + -
243A ILE* 3.9 12.8 - - + +
244A ALA* 4.2 9.2 - - + +
247A ILE* 3.5 32.5 - - + +
249A GLU* 1.3 79.6 - - - +
251A LEU* 1.3 70.7 + - - +
252A ILE* 4.3 9.9 - - + -
271A LEU 3.6 1.2 - - - +
273A LEU* 2.8 49.0 + - + +
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Residues in contact with LEU 251 (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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115A ALA* 4.1 17.7 - - + +
118A LEU* 4.6 11.0 - - + -
119A ALA* 4.7 2.5 - - + -
185A MET* 3.6 29.2 - - + -
218A LEU* 4.1 14.8 - - + +
219A PRO 3.0 13.9 + - - +
220A LEU* 3.3 12.9 - - + +
221A ILE* 2.8 27.9 + - - +
250A VAL* 1.3 83.7 - - - +
252A ILE* 1.3 62.8 + - - +
253A ALA 4.2 0.4 - - - -
270A LEU* 4.2 13.0 - - + -
271A LEU 3.3 1.3 - - - +
272A ALA* 3.9 20.2 - - + -
6B LEU* 3.9 23.1 - - + -
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Residues in contact with ILE 252 (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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87A ILE* 4.1 31.2 - - + -
88A LEU* 4.1 14.4 - - + -
221A ILE* 3.5 11.0 - - + +
223A LEU* 4.5 10.5 - - + -
240A THR* 3.4 31.9 - - + -
244A ALA* 5.4 0.4 - - + -
250A VAL* 4.3 12.8 - - + -
251A LEU* 1.3 76.9 - - - +
253A ALA* 1.3 62.0 + - - +
254A ALA* 4.4 8.1 - - + +
269A CYS 3.6 1.4 - - - +
270A LEU* 3.2 9.2 - - - +
271A LEU* 2.7 55.9 + - + +
273A LEU* 4.5 12.3 - - + -
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Residues in contact with ALA 253 (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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108A GLY* 4.5 2.3 - - - +
111A ALA* 3.7 21.3 - - + +
112A LEU* 3.5 34.1 - - + +
115A ALA* 5.3 0.9 - - + -
220A LEU* 4.4 8.3 - - + -
221A ILE 2.8 12.9 + - - +
222A ASP* 3.7 6.1 - - - +
223A LEU 3.0 23.7 + - - +
251A LEU 4.1 0.8 + - - -
252A ILE* 1.3 70.8 - - - +
254A ALA* 1.3 62.0 + - - +
255A SER* 5.6 0.2 - - - -
269A CYS 3.9 4.3 - - - -
270A LEU* 4.6 0.2 - - - +
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Residues in contact with ALA 254 (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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83A MET* 4.1 14.1 - - + -
87A ILE* 3.6 31.2 - - + -
108A GLY* 3.4 11.5 - - - -
111A ALA* 4.3 0.3 - - - +
223A LEU* 3.2 12.3 - - + +
252A ILE* 3.8 4.8 - - + -
253A ALA* 1.3 74.6 - - - +
255A SER* 1.3 61.9 + - - +
268A GLY* 3.3 4.4 - - - -
269A CYS* 3.0 34.4 + - - +
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Residues in contact with SER 255 (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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83A MET* 5.1 1.9 - - - +
108A GLY* 4.0 2.0 - - - -
223A LEU 3.1 9.8 + - - +
224A ALA* 3.9 24.4 - - - +
254A ALA* 1.3 77.9 - - - +
256A CYS* 1.3 67.6 + - - +
257A SER* 3.2 11.8 + - - -
258A LYS* 4.5 2.9 + - - +
259A ASN* 3.7 13.7 + - - +
267A THR 4.0 4.3 - - - -
413A PLP 2.6 44.6 + - - -
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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