Contacts of the strand formed by residues 311 - 319 (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 ARG 311 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A TRP* 3.7 18.0 + - - +
80A LEU 3.5 20.2 + - - -
81A ARG* 3.9 45.4 - - - +
82A PRO* 4.7 5.7 - - - +
309A PRO 4.7 2.5 - - - +
310A LEU* 1.3 78.3 - - - +
312A VAL* 1.3 62.8 + - - +
342A LEU 3.5 4.9 - - - +
343A ARG* 4.0 36.5 - - + +
350A PHE* 4.1 16.6 - - + -
388A MET* 3.3 41.2 + - + +
390A PRO* 4.1 5.1 - - + +
391A ASP* 3.0 38.3 + - - +
392A VAL 3.0 10.2 + - - +
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Residues in contact with VAL 312 (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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310A LEU* 4.7 6.1 - - + +
311A ARG* 1.3 81.2 - - - +
313A LEU* 1.3 69.4 + - - +
340A LEU 4.0 0.2 - - - +
341A GLY* 3.3 5.5 - - - -
342A LEU* 2.9 50.2 + - + +
344A TRP* 4.9 12.1 - - + -
388A MET* 4.4 3.5 - - - +
392A VAL* 3.6 24.7 - - + +
394A THR* 4.3 9.9 - - + +
520A LEU* 4.1 19.0 - - + +
523A LEU* 4.3 13.7 - - + -
529A LEU* 4.9 12.8 - - + -
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Residues in contact with LEU 313 (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* 1.3 74.0 - - - +
314A SER* 1.3 66.0 + - - +
315A PHE* 4.5 24.0 - - + -
339A SER* 4.2 11.2 - - - +
340A LEU 3.5 15.3 - - - +
381A TRP* 4.7 6.1 - - + -
384A PHE* 4.0 18.8 - - + -
385A ILE* 3.6 24.2 - - + -
388A MET* 3.9 24.5 - - + -
390A PRO* 4.3 12.8 - - + +
392A VAL 3.0 13.0 + - - +
393A ILE* 3.7 13.9 - - + -
394A THR* 2.9 31.4 + - - -
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Residues in contact with SER 314 (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* 1.3 73.3 + - - +
315A PHE* 1.3 63.0 + - - +
339A SER* 3.3 3.8 - - - -
340A LEU* 2.9 34.7 + - - +
394A THR* 2.9 30.0 + - - -
395A GLY* 4.8 4.3 - - - -
516A ALA* 3.7 22.1 - - - +
519A PRO* 5.3 2.2 - - - -
520A LEU* 3.2 29.8 + - - +
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Residues in contact with PHE 315 (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* 4.5 8.1 - - + -
314A SER* 1.3 78.9 - - - +
316A ASP* 1.3 69.7 + - - +
317A ILE* 3.9 25.4 - - + -
337A ILE* 4.4 5.4 - - + -
338A CYS 3.1 12.8 - - - +
339A SER* 3.9 12.3 - - - +
381A TRP* 4.2 24.2 - + + -
393A ILE* 4.2 22.7 - - + -
394A THR 3.9 7.9 + - - -
395A GLY* 4.5 6.6 - - - -
396A TYR 5.3 0.7 + - - -
398A ILE* 3.8 36.1 - - + +
402A ASP* 4.1 15.7 - - + -
403A LEU* 4.1 22.0 - - + -
406A LEU* 4.2 10.1 - - + -
516A ALA* 4.1 6.8 - - - +
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Residues in contact with ASP 316 (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* 1.3 81.0 - - - +
317A ILE* 1.3 80.5 + - - +
318A GLU* 3.8 10.7 - - - +
337A ILE* 3.5 2.9 - - - +
338A CYS 3.0 30.1 + - - -
396A TYR* 4.9 8.8 + - - +
398A ILE* 6.0 0.2 - - - +
402A ASP* 4.7 10.7 - - - +
512A CYS* 4.0 11.0 - - - -
515A ASP* 4.0 23.1 - - - +
516A ALA* 3.9 21.0 - - + +
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Residues in contact with ILE 317 (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* 3.9 21.3 - - + -
316A ASP* 1.3 86.0 - - - +
318A GLU* 1.3 76.3 + - - +
319A CYS* 3.9 23.1 - - - -
334A VAL* 4.4 15.5 - - + -
336A GLN 3.3 9.2 - - - +
337A ILE* 4.2 13.0 - - + -
401A PHE* 4.4 12.0 - - + -
402A ASP* 3.2 35.1 + - - +
405A TYR* 4.5 12.3 - - + -
406A LEU* 4.5 13.9 - - + -
512A CYS* 4.6 0.2 - - - -
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Residues in contact with GLU 318 (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* 3.8 10.9 - - - +
317A ILE* 1.3 83.9 - - - +
319A CYS* 1.3 66.6 + - - +
334A VAL* 3.6 7.4 - - - +
335A ILE* 3.0 43.5 + - + -
336A GLN* 2.9 20.6 + - + +
494A ILE* 3.6 29.4 - - + +
508A LEU* 4.8 11.7 - - + -
511A TYR* 5.0 8.0 - - - -
512A CYS* 3.9 27.5 - - + +
515A ASP* 4.6 7.6 - - - +
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Residues in contact with CYS 319 (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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317A ILE* 3.9 19.7 - - - -
318A GLU* 1.3 81.1 + - - +
320A ALA* 1.3 61.4 - - - +
321A GLY 3.9 2.1 + - - -
327A PRO* 4.6 16.3 - - + +
332A ASP* 4.8 1.1 - - + +
333A PRO 3.4 13.2 - - - +
334A VAL* 4.5 1.6 - - - -
335A ILE* 4.2 5.2 - - - -
401A PHE* 4.4 15.0 - - - -
405A TYR* 3.8 36.3 - - + +
491A HIS* 5.0 9.5 - - - +
494A ILE* 4.3 15.2 - - - +
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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