Contacts of the strand formed by residues 241 - 244 (chain D) in PDB entry 3H3B
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 MET 241 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42D TYR* 2.5 44.0 + - + +
52D LEU* 3.9 7.3 - - - +
95D GLN* 3.5 38.0 + - + +
102D TRP* 3.8 15.7 - - + -
104D PHE* 3.7 22.9 - - + -
169D ASN* 3.7 43.3 - - - +
171D VAL* 4.5 4.7 - - - -
181D TRP* 4.5 7.0 - - + -
231D VAL* 3.7 27.1 - - + -
232D ARG 3.2 6.5 - - - -
233D SER* 3.7 1.7 - - - -
240D ALA* 1.3 72.1 - - - +
242D ASP* 1.3 60.5 + - - +
244D TRP* 5.0 1.8 - - + -
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Residues in contact with ASP 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D LYS* 5.0 2.1 - - - +
52D LEU* 3.8 35.0 + - + +
61D LYS* 4.5 8.4 - - - -
166D TYR* 4.9 1.2 - - - -
232D ARG* 2.8 57.8 + - - +
233D SER* 5.0 0.8 - - - -
238D GLU* 4.4 16.1 - - - +
240D ALA 3.3 6.7 + - - +
241D MET* 1.3 73.5 - - - +
243D TYR* 1.3 94.5 + - + -
244D TRP* 3.7 13.4 + - - -
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Residues in contact with TYR 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D LYS* 3.1 32.4 + - - -
134D SER 5.2 8.5 - - - -
136D VAL* 3.5 53.9 - - + +
138D LEU* 3.4 10.8 - - + +
231D VAL* 3.4 5.3 - - - -
232D ARG* 2.9 47.6 + - + -
242D ASP* 1.3 101.1 + - + +
244D TRP* 1.3 61.2 + - - +
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Residues in contact with TRP 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D TYR* 3.5 33.1 - + + -
49D SER* 4.5 6.6 + - - +
50D PRO* 3.5 55.3 + - + +
51D LYS* 4.6 0.4 - - - -
104D PHE* 4.0 24.7 - + - -
138D LEU* 4.5 7.0 + - - +
171D VAL* 3.8 39.0 - - + -
173D LYS* 6.3 0.4 - - + -
179D PRO* 4.9 4.0 - - + -
229D TYR* 3.6 28.0 - + + -
230D CYS 3.7 4.0 - - - -
231D VAL* 3.6 29.2 - - + +
241D MET* 5.0 2.0 - - - -
242D ASP 3.7 12.3 + - - -
243D TYR* 1.3 75.0 - - - +
245D GLY* 1.3 69.4 + - - +
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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