Contacts of the strand formed by residues 242 - 246 (chain A) in PDB entry 1YA8
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 ARG 242 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A GLY 5.6 0.8 + - - -
214A SER* 3.8 14.9 + - - +
215A VAL 3.6 1.8 + - - +
216A THR* 3.3 28.9 - - + +
217A ILE 3.2 20.3 + - - -
240A PHE* 3.3 11.9 - - - -
241A HIS* 1.3 104.3 + - - +
243A ALA* 1.3 66.0 + - - +
344A VAL* 4.4 1.8 - - - -
345A PRO* 3.7 18.7 - - + +
503A PHE* 3.0 30.3 - - + +
504A ALA* 3.0 16.8 + - - +
505A ARG 3.3 20.3 + - - -
506A ASN 3.7 19.1 + - - -
507A GLY* 3.8 7.2 - - - -
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Residues in contact with ALA 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ILE* 3.2 13.0 - - + +
227A VAL* 3.7 21.3 - - + -
231A VAL* 4.1 13.0 - - + -
240A PHE* 4.2 5.6 - - + -
242A ARG* 1.3 78.4 - - - +
244A ILE* 1.3 57.7 - - - +
344A VAL* 4.7 2.0 - - + -
345A PRO 3.2 7.8 + - - +
346A TYR* 3.2 15.8 - - + -
347A MET 2.8 29.8 + - - -
503A PHE* 3.5 4.2 - - - -
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Residues in contact with ILE 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A MET* 4.6 8.3 - - + -
216A THR* 4.6 5.2 - - + -
217A ILE 3.0 4.8 + - - -
218A PHE* 3.4 32.8 - - + -
219A GLY 3.4 5.4 + - - -
227A VAL* 3.6 7.7 - - - +
243A ALA* 1.3 78.7 - - - +
245A SER* 1.3 71.0 + - - +
246A GLU* 4.4 7.9 - - + -
346A TYR* 4.4 0.2 - - - -
347A MET* 3.1 32.5 - - + +
447A TYR* 4.9 1.3 - - + -
500A TRP* 3.5 46.2 - - + +
503A PHE* 3.6 29.2 - - + -
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Residues in contact with SER 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A GLY 3.9 2.7 - - - -
224A GLY* 3.2 16.6 + - - -
227A VAL* 3.7 5.2 - - - +
244A ILE* 1.3 75.0 - - - +
246A GLU* 1.3 60.5 + - - +
247A SER 3.6 0.6 + - - -
248A GLY 3.5 19.0 + - - -
249A VAL* 4.3 6.1 - - - -
346A TYR* 2.8 33.8 + - - -
347A MET 2.7 10.6 + - - +
348A VAL* 3.7 3.3 - - - +
349A GLY* 3.0 27.7 + - - +
447A TYR* 4.3 1.7 + - - -
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Residues in contact with GLU 246 (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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138A TRP* 3.6 22.5 - - - -
218A PHE* 3.7 5.4 - - - +
219A GLY 2.9 15.8 + - - +
220A GLU* 3.2 5.7 - - + +
221A SER 3.0 21.9 + - - -
224A GLY* 4.4 0.4 - - - -
244A ILE* 4.4 6.9 - - + +
245A SER* 1.3 71.0 - - - +
247A SER* 1.3 70.2 + - - +
248A GLY 3.6 0.2 - - - -
447A TYR* 3.3 22.4 - - - +
471A GLU* 2.7 32.4 - - - +
472A LEU* 3.6 15.4 - - - +
475A VAL* 4.0 10.5 - - - +
500A TRP* 3.1 31.7 + - + -
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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
------------------------------------------------------------
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