Contacts of the strand formed by residues 250 - 255 (chain A) in PDB entry 1YAA
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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219A ALA* 3.7 6.7 - - + +
221A PHE* 3.8 34.3 - - + -
242A VAL* 4.0 31.6 - - + +
244A LEU* 4.0 25.6 - - + -
245A SER* 6.2 0.4 - - - -
248A SER 3.7 12.8 - - - +
249A PRO* 1.3 72.1 - - - +
251A PHE* 1.3 64.1 + - - +
252A VAL* 3.9 7.0 + - + +
269A ALA* 2.9 52.7 + - - +
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Residues in contact with PHE 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 SER* 4.0 9.0 - - - +
118A PHE* 4.3 14.1 - + - -
119A PHE* 3.3 39.9 - + - -
218A ILE* 3.8 15.3 - - + -
219A ALA 3.0 6.6 + - - +
220A LEU* 3.4 19.9 - - + +
221A PHE* 2.9 27.4 + - - +
249A PRO* 3.6 23.1 - - + -
250A VAL* 1.3 73.6 - - - +
252A VAL* 1.3 63.0 + - - +
253A CYS* 4.2 0.9 - - - -
269A HIS* 3.4 61.5 - + + +
6B PHE* 3.8 17.3 - + - -
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Residues in contact with VAL 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* 3.6 27.1 - - + -
88A PHE* 3.9 23.1 - - + -
221A PHE* 3.7 4.5 - - + +
223A THR* 3.8 20.2 - - - +
240A VAL* 4.0 22.4 - - + -
250A VAL* 4.4 12.6 - - + +
251A PHE* 1.3 79.2 - - - +
253A CYS* 1.3 66.6 + - - +
254A GLN 4.5 0.7 - - - +
269A HIS* 2.8 56.9 - - - +
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Residues in contact with CYS 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* 4.3 4.2 - - - +
111A ALA* 3.7 34.8 - - + -
112A LEU* 3.7 34.1 - - + -
115A SER* 3.7 12.8 - - - -
220A LEU* 4.1 12.3 - - - -
221A PHE 3.0 11.1 + - - +
222A ASP* 4.0 6.7 - - - +
223A THR* 2.7 34.9 + - - +
252A VAL* 1.3 74.0 - - - +
254A GLN* 1.3 58.1 + - - +
269A CYS* 3.9 6.5 - - - -
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Residues in contact with GLN 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 ALA* 3.1 37.8 + - - +
86A ILE* 3.6 17.4 - - - +
87A ILE* 3.2 28.9 - - + +
107A SER 4.2 0.7 - - - -
108A GLY* 4.1 5.9 + - - -
111A ALA* 4.6 0.2 - - - +
223A THR* 3.5 9.0 - - + +
226A GLN* 4.2 1.2 + - - +
252A VAL* 3.6 2.6 + - + -
253A CYS* 1.3 73.2 - - - +
255A SER* 1.3 65.5 + - - +
256A PHE* 3.9 12.7 - - + -
259A ASN* 6.0 1.3 - - - +
268A GLY* 3.1 5.8 - - - -
269A CYS* 2.8 78.7 + - - +
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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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107A SER* 3.4 0.7 + - - -
108A GLY* 3.6 9.2 - - - +
223A THR 3.1 11.8 + - - +
224A ALA* 4.0 28.9 + - - +
226A GLN 5.8 0.2 + - - -
253A CYS 5.5 0.2 - - - -
254A GLN* 1.3 79.0 - - - +
256A PHE* 1.3 64.5 + - - +
257A ALA* 3.1 17.9 + - - +
258A LYS* 4.6 1.2 + - - +
259A ASN* 3.6 15.9 + - - +
267A VAL 4.0 3.6 - - - -
905A PLP 2.8 29.6 + - - -
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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