Contacts of the strand formed by residues 293 - 304 (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 ARG 293 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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940B GLU* 6.2 1.2 - - - +
1012B PRO* 4.3 22.2 - - - +
1014B TYR* 2.7 31.3 + - - -
1021B GLU* 3.3 42.4 + - - +
229C LEU* 4.0 25.0 + - + +
230C LEU 3.7 2.0 - - - -
231C PRO* 3.8 23.8 - - - +
232C GLN* 4.3 2.2 - - - +
275C VAL* 4.8 18.2 + - - +
291C LEU* 6.1 3.3 - - + +
292C GLY* 1.3 83.2 + - - +
294C VAL* 1.3 61.6 + - - +
295C ARG* 3.0 32.8 + - - +
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Residues in contact with VAL 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C LEU* 3.3 21.7 - - - +
230C LEU* 3.0 27.6 + - + +
232C GLN* 3.6 27.6 - - + -
293C ARG* 1.3 71.3 - - - +
295C ARG* 1.3 58.2 + - - +
296C ASN* 3.2 15.4 + - + +
297C HIS* 3.5 38.2 + - + +
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Residues in contact with ARG 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1021B GLU* 5.2 7.6 - - + +
59C ILE 4.0 4.0 - - - +
60C ASP* 5.2 2.6 - - - +
61C THR* 4.9 6.7 - - + +
229C LEU* 3.8 16.4 - - + -
292C GLY* 6.0 0.2 - - - -
293C ARG 3.0 24.2 + - - +
294C VAL* 1.3 72.8 - - - +
296C ASN* 1.3 58.2 + - - +
297C HIS 3.9 0.2 - - - -
298C PHE* 4.0 15.2 - - - -
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Residues in contact with ASN 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C ILE* 4.4 1.4 - - - +
58C ASN* 2.3 61.1 + - - +
59C ILE 3.1 30.6 + - - +
294C VAL* 3.1 8.4 - - + +
295C ARG* 1.3 80.2 - - - +
297C HIS* 1.3 60.1 + - - +
298C PHE* 3.9 5.9 - - - -
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Residues in contact with HIS 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ASN* 6.0 0.4 + - - -
55C ASP* 5.2 2.4 - - + +
57C ILE* 3.3 40.6 - - + +
229C LEU* 3.8 5.7 - - - -
230C LEU* 3.3 62.5 + - + +
271C ARG* 5.7 2.0 - - + -
294C VAL* 3.5 22.2 + - + +
296C ASN* 1.3 78.5 - - - +
298C PHE* 1.3 67.6 + - - +
299C ILE* 3.6 23.9 - - + +
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Residues in contact with PHE 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C LEU 2.8 38.8 + - - +
57C ILE* 3.7 5.5 - - - +
59C ILE* 3.1 41.5 - - + -
60C ASP 4.1 0.9 - - - -
61C THR* 3.5 39.3 - - + -
64C ALA* 3.9 18.2 - - + -
65C ASN* 5.2 2.9 - - - -
227C TYR* 4.7 16.6 - + + -
228C ARG 4.3 5.6 - - - -
229C LEU* 4.2 21.3 - - + -
295C ARG 4.0 12.3 - - - -
296C ASN 3.9 7.9 - - - -
297C HIS* 1.3 78.6 + - - +
299C ILE* 1.3 70.9 + - - +
300C PHE* 4.2 13.9 - - + -
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Residues in contact with ILE 299 (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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53C ASN* 4.7 2.9 - - - +
54C PHE 3.3 9.2 - - - +
55C ASP* 3.2 20.4 - - - +
227C TYR* 3.8 18.7 - - - +
228C ARG* 3.4 57.3 + - + +
230C LEU* 5.4 3.8 - - + +
271C ARG* 5.0 12.6 - - + -
297C HIS* 3.6 20.4 - - + +
298C PHE* 1.3 79.6 - - - +
300C PHE* 1.3 68.0 + - - +
301C ASN* 3.2 30.0 + - - +
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Residues in contact with PHE 300 (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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52C ALA 4.6 0.7 - - - -
53C ASN* 2.8 22.7 - - - +
54C PHE* 2.6 48.2 + + + -
56C LEU* 3.5 42.8 - - + -
64C ALA* 4.9 10.3 - - + -
67C PHE* 4.9 9.6 - + + -
71C MET* 6.3 3.1 - - + -
227C TYR* 3.2 57.9 - + + -
298C PHE* 4.2 12.6 - - + -
299C ILE* 1.3 79.9 - - - +
301C ASN* 1.3 64.5 + - - +
302C VAL* 4.3 7.4 - - + -
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Residues in contact with ASN 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
940B GLU 5.2 4.5 - - - +
941B THR 5.8 2.7 - - - +
51C GLU* 3.9 10.6 + - - +
52C ALA 3.7 3.6 - - - -
53C ASN* 2.7 39.8 + - - +
224C THR* 3.7 10.9 + - - +
226C SER 3.9 26.5 + - - +
227C TYR* 4.6 1.2 - - - -
228C ARG* 4.6 3.8 + - - +
299C ILE* 3.2 23.7 - - - +
300C PHE* 1.3 75.5 + - - +
302C VAL* 1.3 67.2 + - - +
303C GLU* 4.4 3.2 - - - +
173N THR* 3.8 26.6 - - + +
174N GLY 4.7 3.2 - - - +
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Residues in contact with VAL 302 (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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51C GLU* 3.4 5.3 + - - +
52C ALA* 2.9 40.9 + - + +
54C PHE* 6.4 1.3 - - + -
71C MET* 5.3 20.4 - - + -
222C VAL* 4.7 12.6 - - + -
224C THR 4.0 7.6 - - - +
225C ALA* 4.8 10.5 - - + -
227C TYR* 5.4 8.5 - - + +
300C PHE* 5.4 6.5 - - + -
301C ASN* 1.3 80.9 - - - +
303C GLU* 1.3 66.2 + - - +
310C PRO* 3.7 27.8 - - + +
313C ILE* 5.7 2.9 - - + -
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Residues in contact with GLU 303 (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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50C ARG 3.6 16.2 - - - +
51C GLU* 3.8 16.1 - - + +
222C VAL* 3.3 8.0 - - - +
223C SER* 3.0 35.6 + - - +
224C THR* 2.3 44.1 + - - +
301C ASN* 4.4 2.6 - - - +
302C VAL* 1.3 83.8 + - - +
304C SER* 1.3 64.6 + - - +
310C PRO* 5.0 2.7 - - - -
12J LYS* 5.5 4.5 - - + -
42J LYS* 6.3 1.3 - - - -
43J ARG* 2.6 28.6 + - - +
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Residues in contact with SER 304 (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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49C ALA 6.0 0.4 - - - -
50C ARG* 3.7 24.7 + - - +
221C PRO 3.2 15.4 + - - -
222C VAL* 4.4 7.4 - - - +
223C SER* 4.5 8.5 + - - -
303C GLU* 1.3 79.1 - - - +
305C ALA* 1.3 62.7 + - - +
306C GLY 3.6 2.7 - - - -
308C MET* 3.2 31.9 + - - +
309C THR 4.1 0.3 - - - -
310C PRO* 3.7 23.6 - - - +
313C ILE* 5.2 1.4 - - - +
13J VAL* 5.9 0.2 - - - +
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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