Contacts of the strand formed by residues 242 - 247 (chain D) in PDB entry 3MSS
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 ILE 242 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494C GLU* 5.0 2.9 - - - +
237D MET* 3.6 40.8 - - + -
238D GLU 4.7 1.3 - - - +
239D ARG* 2.9 23.2 + - - +
240D THR* 3.1 4.7 - - - +
241D ASP* 1.3 83.3 - - + +
243D THR* 1.3 66.0 + - - +
244D MET* 3.6 34.8 + - + +
259D GLY* 4.8 1.8 - - - -
260D VAL 3.4 8.5 - - - +
261D TRP* 3.9 14.1 - - + -
268D VAL* 4.5 11.2 - - + -
270D VAL* 4.1 10.3 - - + -
312D TYR* 4.4 9.1 - - + -
314D ILE* 4.7 13.5 - - + -
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Residues in contact with THR 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494C GLU* 4.2 18.8 + - + +
498C GLN* 3.4 24.2 + - + +
242D ILE* 1.3 70.8 - - - +
244D MET* 1.3 71.1 + - - +
245D LYS* 3.6 13.0 + - + +
259D GLY* 3.2 3.1 - - - -
260D VAL* 2.8 43.0 + - + +
262D LYS* 3.4 29.8 - - - +
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Residues in contact with MET 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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491C GLN* 4.7 11.7 + - - +
494C GLU* 4.8 7.2 + - - +
242D ILE* 3.6 20.7 + - + +
243D THR* 1.3 77.9 - - - +
245D LYS* 1.3 67.6 + - - +
257D TYR* 3.6 41.1 - - + -
258D GLU 4.1 1.3 - - - +
270D VAL* 3.8 36.1 - - + +
272D THR* 4.9 3.8 - - + -
312D TYR* 3.4 32.8 - - + +
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Residues in contact with LYS 245 (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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491C GLN* 5.4 8.1 + - - +
243D THR* 4.2 14.1 - - + +
244D MET* 1.3 81.1 - - - +
246D HIS* 1.3 73.6 + - + +
257D TYR* 3.4 15.6 - - - -
258D GLU* 2.8 46.6 + - - +
260D VAL* 3.5 33.6 - - + +
267D THR* 5.4 1.6 + - - -
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Residues in contact with HIS 246 (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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245D LYS* 1.3 78.1 - - + +
247D LYS* 1.3 83.7 + - - +
248D LEU* 4.7 7.4 - - + -
249D GLY 5.5 1.8 + - - -
257D TYR* 3.5 1.3 - - - -
258D GLU* 3.0 63.7 + - + -
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Residues in contact with LYS 247 (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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246D HIS* 1.3 86.7 + - - +
248D LEU* 1.3 62.8 + - - +
249D GLY 3.8 0.9 + - - -
250D GLY* 4.2 7.1 + - - -
251D GLY* 4.2 21.8 + - - +
254D GLY* 3.5 24.8 + - - +
255D GLU* 2.8 29.4 + - - -
256D VAL 3.5 6.3 - - - +
257D TYR* 3.3 33.4 - - + -
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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