Contacts of the strand formed by residues 334 - 343 (chain A) in PDB entry 6S1M
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 334 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317A ILE* 4.4 18.6 - - + -
318A GLU 3.6 11.4 - - - +
319A CYS* 4.5 0.7 - - - +
333A PRO* 1.3 71.4 - - - +
335A ILE* 1.3 62.2 + - - +
336A GLN 4.5 1.6 - - - +
337A ILE* 4.4 24.7 - - + -
357A LEU* 3.2 19.6 - - - +
374A GLU* 3.9 9.1 + - - +
377A LEU* 3.8 7.4 - - + +
378A LEU* 5.5 6.7 - - + -
405A TYR* 3.6 34.5 - - + -
406A LEU* 4.5 14.8 - - + -
409A ARG* 4.2 15.8 - - + +
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Residues in contact with ILE 335 (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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318A GLU* 3.0 30.4 + - + +
319A CYS* 4.1 5.8 - - - +
320A ALA* 4.3 21.1 - - + -
333A PRO* 4.2 17.0 - - + +
334A VAL* 1.3 76.9 - - - +
336A GLN* 1.3 71.4 + - + +
356A THR* 3.7 1.4 - - - -
357A LEU* 3.3 38.0 + - + +
377A LEU* 4.1 3.5 - - - +
494A ILE* 4.4 7.4 - - + -
498A GLN* 3.7 46.6 + - + +
508A LEU* 4.4 12.8 - - + -
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Residues in contact with GLN 336 (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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316A ASP 4.1 0.2 - - - +
317A ILE* 3.3 5.9 - - - +
318A GLU* 2.9 38.3 + - + +
334A VAL* 3.8 0.9 - - - +
335A ILE* 1.3 92.5 - - + +
337A ILE* 1.3 65.6 + - - +
338A CYS* 4.4 4.0 - - - -
355A LEU 3.4 4.7 - - - +
356A THR* 3.7 31.6 - - + +
377A LEU* 4.7 0.4 - - - +
498A GLN* 5.9 2.1 - - + +
505A ARG* 3.6 30.1 + - - +
508A LEU* 3.8 25.7 - - + +
509A ALA* 3.5 22.4 + - - +
512A CYS* 4.1 11.4 - - - +
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Residues in contact with ILE 337 (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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315A PHE* 4.4 8.1 - - + -
316A ASP 3.5 8.7 - - - +
317A ILE* 4.2 12.3 - - + -
334A VAL* 4.4 13.9 - - + -
336A GLN* 1.3 79.1 - - - +
338A CYS* 1.3 66.4 + - - +
339A SER* 4.6 3.1 + - - +
353A LEU 4.5 0.3 - - - +
354A ALA* 3.7 0.3 - - - -
355A LEU* 2.9 39.5 + - + +
377A LEU* 4.4 23.1 - - + +
378A LEU* 5.0 5.8 - - + -
381A TRP* 4.0 52.0 - - + +
406A LEU* 4.5 18.4 - - + -
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Residues in contact with CYS 338 (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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315A PHE* 3.1 5.5 - - - +
316A ASP 3.0 31.6 + - - -
336A GLN* 4.4 9.9 - - - -
337A ILE* 1.3 80.8 - - - +
339A SER* 1.3 62.2 + - - +
353A LEU 3.6 5.2 - - - +
354A ALA* 3.7 22.2 - - - -
355A LEU 4.9 0.9 - - - -
356A THR* 6.1 0.4 - - - -
509A ALA* 4.3 4.9 - - - -
512A CYS* 3.6 40.6 - - - +
513A LEU* 4.3 18.6 - - + -
516A ALA* 3.7 5.9 - - + +
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Residues in contact with SER 339 (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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313A LEU* 4.2 16.4 - - - +
314A SER 3.3 8.7 - - - -
315A PHE* 3.9 5.6 - - - +
337A ILE* 4.6 0.9 - - - +
338A CYS* 1.3 77.1 + - - +
340A LEU* 1.3 69.2 + - - +
351A LEU 4.2 0.3 - - - +
352A ARG* 3.7 0.5 - - - -
353A LEU* 2.9 44.3 + - - +
355A LEU* 5.9 0.7 - - - +
381A TRP* 3.6 25.1 + - - -
384A PHE* 4.3 12.2 - - - -
516A ALA* 5.2 0.2 - - - -
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Residues in contact with LEU 340 (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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312A VAL 4.0 0.2 - - - +
313A LEU* 3.5 7.5 - - - +
314A SER* 2.9 34.3 + - - +
339A SER* 1.3 80.8 - - - +
341A GLY* 1.3 58.1 + - - +
349A PRO* 4.2 14.6 - - + -
351A LEU 3.4 16.2 - - - +
352A ARG* 3.6 31.4 - - + +
513A LEU* 3.3 44.2 - - + +
516A ALA* 4.4 11.9 - - + +
517A TYR* 4.3 18.6 - - + -
520A LEU* 3.9 18.9 - - + +
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Residues in contact with GLY 341 (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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312A VAL 3.3 8.5 - - - -
313A LEU* 4.8 1.8 - - - -
340A LEU* 1.3 76.6 - - - +
342A LEU* 1.3 62.8 + - - +
349A PRO* 3.7 2.9 - - - +
350A PHE* 3.1 14.2 + - - -
351A LEU* 3.0 41.1 + - - +
388A MET* 4.5 11.9 - - - -
520A LEU* 5.1 0.9 - - - +
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Residues in contact with LEU 342 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310A LEU 3.9 0.2 - - - +
311A ARG* 3.5 3.6 - - - +
312A VAL* 2.9 41.8 + - + +
341A GLY* 1.3 73.9 - - - +
343A ARG* 1.3 82.9 + - - +
344A TRP* 4.2 14.6 - - + -
345A GLY 5.2 0.2 - - - +
346A GLU 4.7 7.6 - - - +
348A GLU 4.3 3.4 - - - +
349A PRO* 3.8 27.8 - - + -
350A PHE* 3.6 13.5 - - - -
388A MET* 5.1 0.8 - - - +
517A TYR* 6.0 0.4 - - + -
520A LEU* 3.8 40.8 - - + -
524A GLU* 5.8 6.5 - - - +
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Residues in contact with ARG 343 (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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79A TRP* 5.5 4.6 - - - +
80A LEU 5.5 1.2 + - - -
309A PRO* 5.1 14.1 - - + +
310A LEU 3.4 7.2 - - - +
311A ARG* 4.0 33.2 - - + +
342A LEU* 1.3 84.3 - - - +
344A TRP* 1.3 64.4 + - - +
345A GLY 3.4 2.3 + - - -
346A GLU* 3.5 51.7 + - + +
348A GLU 5.5 1.0 + - - -
350A PHE* 3.6 45.8 - - + +
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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