Contacts of the strand formed by residues 246 - 252 (chain D) in PDB entry 6CIM
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 ALA 246 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195D TYR* 5.3 1.1 - - - -
237D ARG 3.8 0.7 - - - +
238D VAL* 3.3 3.3 - - - -
239D ASP* 2.9 41.1 + - + +
241D PRO* 4.6 4.2 - - + +
244D THR 5.0 1.3 - - - +
245D PRO* 1.3 75.5 - - - +
247D VAL* 1.3 64.1 + - - +
248D ASN 4.3 0.2 - - - -
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Residues in contact with VAL 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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154D VAL* 6.2 0.2 - - + -
182D VAL* 4.5 11.2 - - + -
184D LEU* 3.9 33.9 - - + -
195D TYR* 4.4 24.8 - - + -
197D LEU* 3.9 31.2 - - + +
236D ILE* 3.8 22.2 - - + -
237D ARG 3.3 9.4 - - - +
238D VAL* 4.2 10.3 - - + -
246D ALA* 1.3 81.6 - - - +
248D ASN* 1.3 64.2 + - - +
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Residues in contact with ASN 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D LEU* 5.1 1.3 - - - -
199D GLU* 3.8 8.7 - - - +
235D ARG 3.9 0.7 - - - +
236D ILE* 3.6 0.7 - - - -
237D ARG* 2.9 50.7 + - + +
246D ALA 4.3 0.2 - - - -
247D VAL* 1.3 77.4 - - - +
249D CYS* 1.3 72.2 + - - +
250D THR* 4.1 17.0 - - - +
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Residues in contact with CYS 249 (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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197D LEU* 3.5 26.5 - - + +
199D GLU* 2.7 40.5 + - + +
200D LEU* 4.2 17.0 - - - -
234D TYR* 3.8 24.9 - - - -
235D ARG 3.1 17.7 - - - +
236D ILE* 3.6 16.6 - - + -
248D ASN* 1.3 77.2 + - - +
250D THR* 1.3 70.9 + - - +
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Residues in contact with THR 250 (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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199D GLU* 4.9 4.3 - - - +
234D TYR* 3.7 0.7 - - - -
235D ARG* 2.9 73.5 + - - +
237D ARG* 5.9 1.3 - - - +
248D ASN* 4.1 17.2 + - - +
249D CYS* 1.3 84.1 - - - +
251D VAL* 1.3 68.1 + - - +
252D LEU* 3.7 3.1 + - - +
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Residues in contact with VAL 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199D GLU* 4.3 22.5 - - + +
232D ASN* 4.4 19.3 - - - +
233D LEU 3.8 7.9 - - - +
234D TYR* 3.9 24.5 - - + -
250D THR* 1.3 74.9 - - - +
252D LEU* 1.3 73.9 + - - +
253D PRO* 4.3 4.2 - - + +
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Residues in contact with LEU 252 (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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217D TYR* 4.2 15.0 - - + -
232D ASN* 5.0 2.4 - - - +
233D LEU* 2.9 53.2 + - + +
235D ARG* 3.7 40.2 - - + +
250D THR* 3.9 20.2 - - - +
251D VAL* 1.3 91.2 - - - +
253D PRO* 1.3 76.9 - - + +
254D GLY 3.8 0.2 + - - -
255D GLY 4.2 1.0 + - - -
297D ILE* 5.6 4.0 - - + +
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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