Contacts of the strand formed by residues 292 - 298 (chain B) in PDB entry 3CME
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 GLY 292 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75B GLU* 4.8 4.7 + - - -
274B GLU* 2.9 34.1 - - - -
275B GLY 2.8 7.5 + - - +
290B VAL* 4.4 1.0 - - - +
291B ASP* 1.3 77.7 - - - +
293B PRO* 1.3 77.3 - - - +
294B TYR* 3.2 9.2 - - - +
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Residues in contact with PRO 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B GLU* 3.4 10.3 - - - +
76B THR* 3.0 23.1 + - - +
77B PRO* 3.4 40.2 - - + +
78B PRO* 4.6 9.9 - - + -
150B ALA* 6.4 0.2 - - + -
273B GLY 3.3 10.1 - - - +
274B GLU* 3.4 20.8 - - + +
292B GLY* 1.3 82.4 - - - +
294B TYR* 1.3 61.4 + - - +
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Residues in contact with TYR 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B VAL* 4.5 8.5 - - + -
74B ILE 3.0 16.6 - - - +
75B GLU* 4.3 1.8 - - - -
76B THR* 3.2 10.6 + - - -
271B ASP* 3.8 20.7 + - - -
272B ILE* 3.5 4.6 - - - +
273B GLY* 2.9 43.8 + - - +
274B GLU* 3.7 25.3 + - - -
275B GLY 4.0 5.4 - - - -
277B GLU* 3.8 16.5 + - - +
278B PRO* 3.2 40.7 - - + +
290B VAL* 4.3 6.1 - - + -
292B GLY 3.2 18.6 - - - +
293B PRO* 1.3 75.4 - - - +
295B THR* 1.3 71.3 + - - +
296B LEU* 4.0 17.6 - - + +
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Residues in contact with THR 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B THR 3.4 2.8 - - - +
73B VAL* 3.6 1.6 - - - -
74B ILE* 2.7 36.8 + - - +
76B THR* 2.9 22.8 + - - -
190B MET* 3.5 20.0 - - - +
269B LEU* 3.9 28.9 - - + -
271B ASP 3.4 9.4 - - - +
272B ILE* 4.1 9.8 - - + +
294B TYR* 1.3 74.7 + - - +
296B LEU* 1.3 69.2 + - - +
297B VAL* 3.6 12.2 + - + -
311B PHE* 4.3 8.1 - - + -
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Residues in contact with LEU 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B THR* 5.4 0.4 - - - +
51B VAL* 5.0 14.6 - - + -
71B VAL* 3.5 26.2 - - + -
72B THR 3.6 2.0 - - - -
73B VAL* 3.5 34.8 - - + -
269B LEU* 3.9 1.6 - - - -
270B ILE* 2.9 31.9 + - + +
271B ASP* 2.8 40.7 + - + +
278B PRO* 3.9 15.5 - - + -
294B TYR* 4.0 11.7 - - + +
295B THR* 1.3 77.6 - - - +
297B VAL* 1.3 61.0 + - - +
327B VAL* 6.1 1.3 - - + -
330B VAL* 5.0 11.2 - - + -
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Residues in contact with VAL 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B VAL* 3.7 1.9 - - - -
72B THR* 2.9 34.7 + - - +
74B ILE* 4.4 7.9 - - + -
202B VAL* 4.6 2.5 - - + -
267B LYS* 3.9 25.4 - - + -
268B ARG 3.9 4.7 - - - +
269B LEU* 4.1 7.4 - - + +
295B THR* 4.0 9.9 - - + +
296B LEU* 1.3 69.3 - - - +
298B LYS* 1.3 76.7 + - - +
299B GLY 3.3 2.1 + - - +
300B SER 4.9 0.2 - - - +
301B VAL* 4.0 23.8 - - + -
311B PHE* 3.3 37.5 - - + -
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Residues in contact with LYS 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27650 C 4.0 19.2 + - - +
27660 A 3.2 27.9 + - - +
69B VAL* 3.5 30.1 - - + -
70B PRO* 3.8 4.5 - - + -
71B VAL* 4.2 0.9 - - - -
199B TYR* 6.3 0.6 - - - -
267B LYS* 3.8 14.0 - - - +
268B ARG* 2.9 43.7 + - + +
270B ILE* 3.7 19.2 - - + +
296B LEU 3.7 2.6 + - - -
297B VAL* 1.3 81.5 - - - +
299B GLY* 1.3 64.2 + - - +
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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