Contacts of the strand formed by residues 215 - 218 (chain A) in PDB entry 4L1O
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 PRO 215 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213A LYS 3.1 7.8 - - - +
214A SER* 1.3 86.2 - - - +
216A CYS* 1.3 58.7 + - - +
217A TYR 4.1 1.1 - - - +
248A TYR* 3.4 37.7 - - + +
250A LEU* 4.4 2.9 - - + -
354A ILE* 3.9 28.7 - - + -
360A PRO* 3.6 9.6 - - + -
362A ALA 3.4 14.4 - - - +
363A LEU* 3.8 18.6 - - + -
364A TYR* 3.0 29.4 + - - +
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Residues in contact with CYS 216 (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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215A PRO* 1.3 75.3 - - - +
217A TYR* 1.3 59.5 - - - +
218A VAL* 3.6 3.9 + - - +
231A ILE* 3.8 21.8 - - - -
246A PRO* 3.8 21.8 - - + -
248A TYR* 2.9 19.4 + - - +
249A ILE* 3.3 10.3 - - + +
250A LEU* 3.0 23.0 + - - +
364A TYR* 3.5 9.4 - - + -
366A PHE* 3.7 36.8 - - - -
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Residues in contact with TYR 217 (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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215A PRO* 4.1 1.0 - - - +
216A CYS* 1.3 71.3 - - - +
218A VAL* 1.3 62.5 + - - +
219A ASP* 3.9 37.0 + - + -
220A LYS 5.1 0.7 + - - -
250A LEU* 3.4 28.0 - - + -
251A CYS* 5.2 1.8 - - - -
252A ASP 5.7 0.4 - - - -
344A VAL* 4.5 9.4 - - + -
346A SER 4.6 0.8 - - - -
347A LEU* 3.7 38.2 + - + +
350A ALA* 3.6 28.9 - - + -
354A ILE* 5.3 1.6 - - + -
364A TYR 3.0 10.0 + - - +
365A MET* 3.2 10.2 - - + -
366A PHE* 2.8 27.5 + - - +
372A VAL* 4.4 10.0 - - + +
376A MET* 3.7 28.7 - - + -
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Residues in contact with VAL 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A CYS* 4.0 11.7 - - - +
217A TYR* 1.3 83.0 - - - +
219A ASP* 1.3 66.6 + - - +
220A LYS 3.8 0.7 + - - -
222A CYS* 4.2 5.8 - - - -
224A LEU* 3.4 31.9 - - + -
227A ALA* 5.0 3.4 - - + -
228A CYS* 5.9 0.4 - - - -
231A ILE* 3.8 28.0 - - + -
249A ILE* 4.1 13.7 - - + -
250A LEU 2.9 17.1 + - - +
251A CYS* 3.9 6.8 - - - -
252A ASP 4.5 1.7 + - - -
255A ILE* 3.8 8.5 - - + +
259A ILE* 3.9 20.0 - - + -
366A PHE* 3.9 8.3 - - + -
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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