Contacts of the strand formed by residues 222 - 231 (chain C) in PDB entry 5M64
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 VAL 222 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71C MET* 4.1 21.1 - - + +
72C ILE* 5.0 8.4 - - + +
220C SER* 3.1 18.8 + - - +
221C PRO* 1.3 82.5 - - + +
223C SER* 1.3 68.8 + - - +
224C THR 3.5 25.6 - - - +
225C ALA* 4.4 11.0 - - + +
302C VAL* 4.7 9.6 - - + -
303C GLU 3.3 18.6 - - - +
304C SER* 4.4 5.4 - - - +
313C ILE* 3.6 33.9 - - + -
6J ARG* 4.9 2.0 + - - -
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Residues in contact with SER 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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944B GLN* 6.2 0.3 - - - +
72C ILE* 5.0 7.5 - - - +
221C PRO 4.3 0.4 + - - -
222C VAL* 1.3 75.7 - - - +
224C THR* 1.3 59.4 + - - +
303C GLU* 3.0 31.8 + - - +
304C SER* 4.5 9.6 + - - +
305C ALA* 4.8 4.2 + - - +
6J ARG* 5.3 1.6 - - - +
9J SER 4.5 2.9 - - - +
10J CYS 2.8 26.2 - - - +
11J GLY* 3.2 27.2 + - - -
12J LYS* 3.7 6.3 + - - +
43J ARG* 3.9 5.2 - - - -
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Residues in contact with THR 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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941B THR 5.0 0.9 + - - -
942B GLY* 3.2 34.4 - - - +
944B GLN* 5.8 1.6 - - + -
72C ILE* 5.6 1.6 - - - -
222C VAL* 3.5 13.4 - - - +
223C SER* 1.3 73.1 - - - +
225C ALA* 1.3 59.7 - - - +
226C SER 4.0 0.7 - - - -
301C ASN 3.7 9.2 + - - +
302C VAL* 4.0 1.2 - - - -
303C GLU* 2.3 38.6 + - - +
9J SER 4.1 2.0 - - - +
10J CYS* 3.2 26.2 - - - +
43J ARG* 3.0 32.5 + - - +
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Residues in contact with ALA 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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938B PHE* 4.8 1.2 - - - -
942B GLY 5.1 0.8 + - - -
944B GLN* 4.4 10.8 + - - +
68C ARG* 3.2 46.1 - - + +
71C MET* 4.5 10.8 - - + -
72C ILE* 4.5 19.0 - - + +
222C VAL* 4.4 11.7 - - + -
224C THR* 1.3 72.9 - - - +
226C SER* 1.3 59.8 + - - +
227C TYR* 5.6 1.8 - - + -
301C ASN 4.3 4.3 - - - -
302C VAL* 4.8 6.5 - - + -
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Residues in contact with SER 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
938B PHE* 3.2 15.2 - - - -
939B SER 2.2 31.9 + - - -
940B GLU* 3.7 5.7 - - - +
941B THR 4.5 2.5 - - - -
942B GLY* 3.6 24.2 - - - -
944B GLN* 5.0 0.2 - - - -
68C ARG* 4.3 1.1 - - - +
224C THR 4.0 0.4 - - - -
225C ALA* 1.3 76.1 - - - +
227C TYR* 1.3 75.7 + - - +
301C ASN* 3.9 27.4 + - - +
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Residues in contact with TYR 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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938B PHE* 3.5 12.1 - + + -
940B GLU* 3.8 2.6 - - - -
1014B TYR* 3.3 19.4 - - - -
64C ALA* 3.1 36.3 - - + -
65C ASN* 4.7 6.3 - - - -
67C PHE* 3.9 4.3 - - - +
68C ARG* 3.4 36.0 + - + -
71C MET* 4.9 6.1 - - - +
225C ALA* 5.2 0.9 - - + -
226C SER* 1.3 94.0 + - - +
228C ARG* 1.3 66.0 + - - +
229C LEU* 6.5 0.2 - - + -
298C PHE* 4.7 12.3 - + + -
299C ILE* 3.8 10.1 - - - +
300C PHE* 3.2 62.5 - + + -
301C ASN 4.7 3.1 - - - -
302C VAL* 5.4 5.8 - - + -
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Residues in contact with ARG 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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940B GLU* 3.6 41.2 + - + +
1014B TYR* 3.5 11.2 - - - +
227C TYR* 1.3 81.3 - - - +
229C LEU* 1.3 69.5 + - - +
230C LEU* 3.7 3.4 + - - +
231C PRO* 4.2 18.0 - - - +
271C ARG* 3.0 37.6 + - - +
273C ASP 4.1 11.7 + - - -
298C PHE* 4.3 4.1 - - - -
299C ILE* 3.4 54.6 + - + +
301C ASN* 4.6 3.8 + - - +
171N PHE* 5.9 1.5 - - - +
172N ALA* 4.3 24.3 - - - +
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Residues in contact with LEU 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1014B TYR* 3.7 22.6 + - + -
1019B GLY 4.9 12.1 - - - +
1021B GLU* 4.6 15.0 - - + +
61C THR* 5.0 7.4 - - + -
228C ARG* 1.3 81.7 + - - +
230C LEU* 1.3 64.8 + - - +
231C PRO* 3.3 11.4 - - - +
293C ARG* 4.0 32.8 + - + +
294C VAL 3.3 23.8 - - - +
295C ARG* 3.8 24.0 - - + -
297C HIS 3.8 6.1 - - - +
298C PHE* 4.2 23.3 - - + -
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Residues in contact with LEU 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228C ARG* 3.7 4.8 + - - +
229C LEU* 1.3 71.2 - - - +
231C PRO* 1.3 74.8 - - + +
232C GLN* 6.4 0.2 - - + -
270C ALA* 3.3 46.7 - - + +
271C ARG* 3.7 12.3 - - + +
293C ARG* 3.7 0.8 - - - -
294C VAL* 3.0 37.8 + - + +
297C HIS* 3.3 63.6 + - + +
299C ILE* 5.4 4.3 - - + -
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Residues in contact with PRO 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228C ARG* 4.2 12.3 - - - +
229C LEU 3.3 10.5 - - - +
230C LEU* 1.3 102.1 - - + +
232C GLN* 1.3 60.3 + - - +
233C ILE* 4.0 2.7 + - - +
270C ALA* 4.0 16.4 - - - +
273C ASP* 3.2 38.8 - - - +
274C THR* 5.5 0.4 - - - -
275C VAL* 3.7 19.1 - - + +
292C GLY 3.6 7.9 - - - +
293C ARG* 3.8 14.8 - - - +
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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