Contacts of the strand formed by residues 325 - 332 (chain A) in PDB entry 1MDF
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 325 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301A GLN 3.0 12.1 + - - -
302A VAL* 3.3 8.3 - - - +
303A LEU 2.9 23.4 + - - -
319A LYS* 6.2 0.2 - - - -
324A CYS* 1.3 79.1 - - - +
326A LEU* 1.3 77.2 + - - +
342A LEU* 4.5 27.4 + - + +
349A ILE* 3.7 20.0 - - + -
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Residues in contact with LEU 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A LEU 3.4 11.9 - - - +
305A VAL* 3.7 27.4 - - + -
310A PHE* 4.2 3.6 - - + -
315A ALA* 3.4 45.5 - - + +
318A VAL* 3.6 27.5 - - + +
319A LYS* 5.4 1.4 - - - +
324A CYS 3.9 2.8 + - - -
325A THR* 1.3 87.4 - - - +
327A GLN* 1.3 82.0 + - - +
328A GLN* 4.3 3.8 - - + +
340A THR* 4.2 0.3 + - - -
341A ARG 5.5 0.2 - - - +
342A LEU* 5.3 0.3 - - - +
346A GLU* 5.6 4.8 + - - +
349A ILE* 3.0 44.6 - - + +
350A VAL* 4.9 1.3 - - + -
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Residues in contact with GLN 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A VAL 4.2 5.9 + - - -
218A CYS* 3.6 21.0 - - - +
275A ILE* 4.9 0.2 - - - +
302A VAL* 3.9 20.6 - - + +
303A LEU 2.8 9.2 + - - +
304A GLN* 2.8 39.0 + - + +
305A VAL 3.1 21.3 + - - -
326A LEU* 1.3 79.1 - - - +
328A GLN* 1.3 69.3 + - - +
329A VAL* 3.6 2.5 + - + -
339A TYR* 3.7 14.4 - - - +
340A THR* 3.1 29.6 + - - +
342A LEU* 3.7 20.9 - - + +
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Residues in contact with GLN 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A VAL 3.3 8.4 + - - +
310A PHE* 3.6 34.3 + - + +
315A ALA* 3.8 7.1 - - - +
326A LEU* 4.4 10.1 - - + -
327A GLN* 1.3 75.3 - - - +
329A VAL* 1.3 60.7 + - - +
330A PHE 4.2 0.4 - - - -
338A ASN 3.7 0.5 - - - +
339A TYR* 3.5 4.9 - - - -
340A THR* 3.0 32.4 + - + -
349A ILE 2.9 26.1 - - - +
350A VAL 3.6 11.8 - - - +
352A THR 3.1 20.5 + - - +
353A GLN* 2.6 39.1 + - - +
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Residues in contact with VAL 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A TYR* 4.1 16.4 - - + +
240A SER* 4.1 11.4 - - - -
304A GLN* 3.6 34.5 - - + +
305A VAL 3.1 7.9 + - - +
306A GLY* 3.1 21.0 - - - -
307A GLY 3.8 4.5 + - - -
308A ALA 5.3 0.5 - - - +
327A GLN* 3.8 11.0 - - + +
328A GLN* 1.3 80.1 - - - +
330A PHE* 1.3 62.3 + - - +
331A GLY* 3.7 5.0 + - - +
337A VAL* 4.0 13.0 - - + -
338A ASN 3.3 6.1 - - - +
339A TYR* 3.8 26.0 - - + -
353A GLN* 5.6 0.2 - - - -
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Residues in contact with PHE 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A GLY 5.6 2.0 - - - +
308A ALA* 6.6 0.7 - - - -
329A VAL* 1.3 71.7 - - - +
331A GLY* 1.3 64.4 + - - +
332A MET* 3.9 15.8 - - + +
336A LEU 4.2 0.5 - - - +
337A VAL* 3.9 0.2 - - - -
338A ASN* 2.9 61.1 + - - +
353A GLN* 3.6 27.0 + - + +
381A LEU* 3.9 17.9 - - + -
413A ASP* 3.4 42.0 - - + -
415A VAL* 4.5 0.4 - - + -
423A ILE* 4.1 14.6 - - + -
425A VAL* 3.6 31.6 - - + -
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Residues in contact with GLY 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A ASN* 5.5 0.2 - - - -
240A SER* 5.6 0.9 - - - -
307A GLY* 5.7 4.7 - - - +
329A VAL* 3.7 7.4 + - - +
330A PHE* 1.3 86.7 - - - +
332A MET* 1.3 64.1 + - - +
336A LEU 3.3 11.0 - - - -
337A VAL* 3.7 17.0 - - - -
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Residues in contact with MET 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A ASN* 3.1 15.5 + - - +
330A PHE* 3.9 33.2 - - + +
331A GLY* 1.3 74.1 - - - +
333A ALA* 1.3 62.5 + - - +
334A GLU* 3.1 15.3 - - + +
335A GLY 3.2 29.4 + - - +
336A LEU* 3.1 45.4 + - + +
337A VAL* 4.5 1.0 - - - +
381A LEU* 4.6 0.2 - - + -
383A THR* 4.6 0.4 - - - -
409A TYR* 3.9 13.9 - - - -
411A THR* 3.8 33.2 - - + +
413A ASP* 4.2 3.1 - - - +
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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