Contacts of the strand formed by residues 313 - 325 (chain C) in PDB entry 2MPR
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 THR 313 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27C GLY 4.4 8.3 + - - +
303C GLN* 4.0 3.3 + - - +
304C ASN* 3.6 2.5 - - - +
305C ILE* 2.9 48.2 + - - +
311C LEU 4.9 0.9 - - - +
312C GLY* 1.3 79.1 - - - +
314C GLU* 1.3 60.4 + - - +
315C TRP* 4.1 3.8 - - - +
341C VAL* 4.0 15.5 - - + -
342C LYS 3.3 11.4 - - - +
343C SER* 4.7 0.2 - - - -
344C GLN* 4.1 3.1 - - - +
386C TRP* 4.0 17.0 - - + -
388C TYR* 3.6 24.2 - - - +
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Residues in contact with GLU 314 (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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302C TYR* 3.2 39.2 + - + +
303C GLN 3.6 3.4 - - - -
304C ASN* 3.7 11.6 - - - +
313C THR* 1.3 71.7 - - - +
315C TRP* 1.3 60.5 + - - +
316C TRP* 3.5 14.3 + - - +
340C ASN 3.7 1.9 - - - +
341C VAL* 3.4 2.8 - - - -
342C LYS* 2.8 61.0 + - + +
349C ARG* 3.1 30.3 + - - -
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Residues in contact with TRP 315 (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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27C GLY 5.3 1.3 - - - +
28C ALA* 3.6 17.2 - - + +
29C GLN* 3.4 36.8 - - + -
30C SER* 3.1 30.5 - - - -
117C PHE* 4.3 6.3 - + - -
301C MET* 3.7 29.0 - - + +
302C TYR* 3.3 7.8 - - - -
303C GLN* 2.7 68.2 + - + +
313C THR* 4.1 4.5 - - - +
314C GLU* 1.3 74.5 - - - +
316C TRP* 1.3 79.7 + - - +
317C THR* 3.8 12.5 - - + -
339C ASP* 3.0 28.9 + - - -
340C ASN 3.5 8.3 - - - -
341C VAL* 3.7 22.4 - - + +
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Residues in contact with TRP 316 (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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301C MET 3.4 8.5 - - - -
302C TYR* 3.4 44.7 - + + -
314C GLU* 3.5 21.3 + - + -
315C TRP* 1.3 80.6 - - - +
317C THR* 1.3 60.8 + - - +
318C VAL* 5.2 7.6 - - + -
338C TYR* 3.8 5.8 - - + +
339C ASP* 3.4 2.4 - - - -
340C ASN* 2.8 50.8 + - + +
349C ARG* 4.2 17.2 - - - +
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Residues in contact with THR 317 (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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30C SER* 5.4 0.2 + - - -
32C TYR* 2.7 28.6 + - - +
115C ILE* 4.8 10.6 - - + +
299C VAL* 5.4 2.7 - - + -
300C GLY* 3.5 1.3 - - - -
301C MET* 2.9 70.4 + - + +
315C TRP* 3.8 12.0 - - + -
316C TRP* 1.3 74.9 - - - +
318C VAL* 1.3 66.0 + - - +
338C TYR 3.2 4.2 + - - -
339C ASP* 2.7 25.2 + - - -
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Residues in contact with VAL 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C TYR* 3.0 5.5 + - - -
299C VAL 3.4 12.8 - - - +
300C GLY* 4.5 6.1 - - - -
316C TRP* 5.2 7.0 - - + -
317C THR* 1.3 82.8 - - - +
319C GLY* 1.3 63.0 + - - +
336C VAL 4.1 0.2 - - - +
337C GLY* 3.4 0.9 - - - -
338C TYR* 2.8 51.9 + - + +
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Residues in contact with GLY 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C TYR* 3.3 16.7 + - - -
114C MET* 4.2 4.5 - - - -
298C TYR* 3.4 4.2 - - - +
299C VAL* 3.0 32.4 + - - +
318C VAL* 1.3 79.4 - - - +
320C VAL* 1.3 63.8 + - - +
336C VAL 3.1 12.3 - - - -
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Residues in contact with VAL 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C MET* 4.0 3.9 - - - +
296C LEU* 3.8 24.9 - - + -
297C MET 3.5 7.0 - - - +
298C TYR* 3.9 10.3 - - + -
319C GLY* 1.3 76.7 - - - +
321C ARG* 1.3 61.7 + - - +
322C PRO* 3.9 13.7 - - + -
334C LEU* 3.8 2.1 - - + +
335C GLU* 3.4 3.6 - - - +
336C VAL* 2.9 44.0 + - + +
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Residues in contact with ARG 321 (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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33C ARG* 4.1 5.3 - - - +
34C LEU* 3.7 28.4 - - - +
113C HIS* 3.3 31.7 + - - -
114C MET* 3.7 29.6 - - + +
296C LEU* 3.6 2.4 - - - -
297C MET* 2.8 45.1 + - + +
320C VAL* 1.3 75.7 - - - +
322C PRO* 1.3 61.9 - - - +
333C LEU* 4.2 24.7 - - + +
334C LEU 3.2 9.0 - - - +
335C GLU* 2.7 43.9 + - + +
367C ILE* 3.4 13.7 + - + +
370C ARG* 4.1 9.3 - - - +
374C ARG* 4.4 9.1 - - - +
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Residues in contact with PRO 322 (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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294C TRP* 4.1 22.0 - - + -
295C ASP 3.4 7.2 - - - +
296C LEU* 3.8 13.9 - - + -
320C VAL* 3.8 16.6 - - + +
321C ARG* 1.3 89.7 - - - +
323C MET* 1.3 60.4 + - - +
324C TYR 4.2 0.2 - - - -
332C THR 4.0 0.7 - - - +
333C LEU* 3.6 4.9 - - - +
334C LEU* 3.0 57.1 + - + +
367C ILE* 4.9 0.2 - - - -
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Residues in contact with MET 323 (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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293C LYS 3.3 0.9 - - - +
294C TRP* 3.2 11.3 - - - -
295C ASP* 2.7 44.2 + - + +
322C PRO* 1.3 74.2 - - - +
324C TYR* 1.3 63.0 + - - +
325C LYS* 4.5 13.8 - - + +
331C SER* 3.2 34.3 - - - +
332C THR 3.6 3.6 - - - -
333C LEU* 4.2 13.0 - - + -
360C GLN* 4.1 6.5 - - - +
362C GLN* 3.7 24.9 - - - +
365C ASP 4.6 2.7 - - - -
366C SER 3.8 12.3 - - - +
367C ILE* 3.4 43.3 - - + -
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Residues in contact with TYR 324 (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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293C LYS* 3.2 40.1 + - + +
294C TRP* 3.5 45.0 - + + -
323C MET* 1.3 72.7 - - - +
325C LYS* 1.3 67.9 + - - +
326C TRP* 3.4 54.6 + + - -
331C SER* 3.0 21.0 - - - -
332C THR* 3.0 24.6 + - - +
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Residues in contact with LYS 325 (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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289C SER* 4.6 3.2 + - - -
291C GLY 5.2 2.4 + - - -
292C ASP 3.6 22.7 + - - +
293C LYS* 2.8 39.8 + - + +
294C TRP 4.3 6.9 + - - -
295C ASP* 3.0 38.9 + - - -
323C MET* 4.5 14.6 - - + +
324C TYR* 1.3 76.2 - - - +
326C TRP* 1.3 66.2 + - - +
327C THR* 3.3 11.8 - - - +
328C PRO* 5.7 0.4 - - + -
330C MET 4.0 4.3 - - - -
331C SER* 4.1 2.2 - - - -
365C ASP* 2.9 43.5 + - + +
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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