Contacts of the strand formed by residues 245 - 248 (chain E) in PDB entry 3W13
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 TYR 245 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52C TRP* 4.1 25.2 - + - -
54C ASP* 2.8 35.2 + - - -
56C ASN* 4.4 7.5 + - - -
31D TYR* 3.8 15.1 + - - -
233E LEU* 3.7 28.7 - - + -
234E ASP* 4.0 12.1 + - - -
241E CYS* 3.9 6.3 - - + +
242E PRO* 2.7 29.0 + - + +
243E PRO* 4.2 1.0 - - - +
244E PRO* 1.3 96.4 - - + +
246E TYR* 1.3 66.9 + - - +
253E CYS* 4.1 14.4 - - + -
254E VAL* 3.2 26.0 - - - +
255E ASN* 3.9 16.6 - - + -
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Residues in contact with TYR 246 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241E CYS* 4.0 4.5 - - - -
243E PRO* 6.4 0.4 - - + -
244E PRO* 3.6 20.6 + - + +
245E TYR* 1.3 79.4 - - - +
247E HIS* 1.3 63.7 + - - +
248E PHE 3.3 2.3 + - - -
253E CYS* 3.4 3.3 - - - -
254E VAL* 2.6 37.4 + - + +
255E ASN 4.1 1.6 - - - -
256E PHE* 3.8 47.1 - + + +
259E CYS* 5.4 2.7 - - + -
279E ILE* 4.2 27.9 - - + +
282E ASN* 3.5 44.1 + - - +
284E CYS* 4.3 19.1 - - + +
300E LEU* 5.3 5.5 - - + +
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Residues in contact with HIS 247 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D TYR* 5.1 0.4 - - - -
33D SER* 3.2 38.3 + - - -
34D ASN* 6.3 0.2 - - + -
231E PHE* 3.2 34.7 - + + -
240E THR* 3.3 10.8 + - - -
241E CYS* 3.1 52.2 + - + +
246E TYR* 1.3 69.4 - - - +
248E PHE* 1.3 59.9 + - - +
249E GLN 4.3 0.2 + - - -
250E ASP* 4.7 7.1 - - - +
282E ASN* 3.0 26.7 + - + +
283E LYS* 3.4 16.4 - - + +
284E CYS 2.9 28.2 + - - +
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Residues in contact with PHE 248 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E GLU* 3.1 37.0 - - - -
231E PHE* 5.3 0.2 - - - -
247E HIS* 1.3 74.3 - - - +
249E GLN* 1.3 80.9 + - + +
250E ASP* 2.7 16.3 + - - +
251E TRP* 3.0 12.5 + - - -
252E ARG* 2.8 40.6 + - + +
254E VAL* 3.8 21.5 - - + -
258E PHE* 3.9 25.6 - + - -
262E LEU* 4.6 7.4 - - + -
277E TYR* 3.7 36.1 - + - -
284E CYS* 3.7 23.8 - - + -
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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