Contacts of the strand formed by residues 351 - 360 (chain A) in PDB entry 1MS4
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 LYS 351 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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347A TYR* 3.1 7.0 - - - -
348A LYS 2.9 34.7 + - - +
349A ASP* 3.5 14.3 + - + +
350A ASP* 1.3 88.3 + - - +
352A LEU* 1.3 60.5 + - - +
353A TYR* 3.3 28.2 - - + +
372A VAL* 6.0 6.1 - - + -
375A LEU* 4.2 4.7 - - + -
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Residues in contact with LEU 352 (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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294A ILE* 5.6 1.3 - - + -
301A LEU* 3.9 19.7 - - + -
319A LEU* 4.3 8.1 - - + -
345A VAL* 4.0 9.0 - - + -
346A LEU 3.5 6.1 - - - +
347A TYR* 3.7 28.7 - - + -
351A LYS* 1.3 74.2 - - - +
353A TYR* 1.3 68.1 + - - +
370A ARG* 3.8 2.8 - - - +
371A LEU* 2.9 56.2 + - + +
374A GLU* 4.5 3.6 - - + -
375A LEU* 4.1 27.9 - - + +
378A ILE* 4.2 24.2 - - + -
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Residues in contact with TYR 353 (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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39A LEU* 3.9 17.3 - - + -
46A MET* 4.7 6.7 - - + -
73A ASP* 4.0 24.9 + - + +
345A VAL* 3.5 8.3 - - - +
346A LEU* 2.8 46.9 + - + +
348A LYS* 3.9 14.8 + - + +
349A ASP* 6.1 0.2 - - - +
351A LYS* 3.3 42.8 - - + +
352A LEU* 1.3 78.4 - - - +
354A CYS* 1.3 64.3 + - - +
368A PHE* 3.2 27.1 - + + -
369A ALA 3.3 11.4 - - - +
370A ARG* 3.7 31.2 + - + -
371A LEU* 4.1 5.3 - - - +
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Residues in contact with CYS 354 (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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39A LEU* 4.3 2.9 - - - -
303A THR* 5.3 1.1 - - - -
317A LEU* 4.3 6.5 - - - -
333A VAL* 4.5 5.4 - - + -
343A SER* 4.0 12.6 - - - -
344A SER 3.3 11.7 - - - +
345A VAL* 4.2 11.4 - - + -
353A TYR* 1.3 76.6 - - - +
355A LEU* 1.3 62.1 + - - +
356A HIS* 3.9 30.3 + - + -
367A VAL 3.7 2.8 - - - +
368A PHE* 3.7 1.3 - - - -
369A ALA* 2.8 38.7 + - + +
371A LEU* 3.8 25.1 - - + -
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Residues in contact with LEU 355 (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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10A LEU* 4.4 2.7 - - + -
11A PHE* 4.2 15.7 - - + -
37A PRO* 3.6 29.7 - - + +
38A ALA 4.2 12.1 - - - +
39A LEU* 3.8 22.8 - - + +
48A ALA* 3.8 26.2 - - + -
49A ILE 4.7 1.8 - - - +
343A SER* 3.3 1.7 - - - -
344A SER 2.8 36.4 + - - +
354A CYS* 1.3 70.5 - - - +
356A HIS* 1.3 64.2 + - - +
366A LEU* 3.9 20.0 - - + -
367A VAL 3.4 18.8 - - - +
368A PHE* 4.2 13.7 - - + +
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Residues in contact with HIS 356 (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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7A ARG* 3.9 10.4 + - - -
37A PRO* 4.5 1.6 - - - -
317A LEU* 3.9 14.3 - - + +
333A VAL* 4.1 10.7 + - + +
334A SER* 3.9 30.4 - - - -
340A SER* 4.1 4.8 - - - -
342A TYR 3.4 10.5 - - - +
343A SER* 3.9 7.2 - - - -
354A CYS* 3.9 22.7 - - + -
355A LEU* 1.3 79.3 - - - +
357A GLU* 1.3 85.9 + - - +
358A ILE* 3.8 11.4 - - + -
366A LEU* 3.0 8.3 - - - -
367A VAL* 2.7 68.1 + - + +
369A ALA* 5.0 3.9 - - + +
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Residues in contact with GLU 357 (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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34A PHE 4.3 2.9 - - - +
35A ARG* 2.8 59.5 + - - +
36A LEU 3.0 9.0 + - - -
37A PRO* 4.2 0.7 - - + -
340A SER* 3.2 16.8 - - - -
341A ALA* 3.6 9.0 - - - +
342A TYR* 2.9 46.7 + - + +
356A HIS* 1.3 87.8 + - - +
358A ILE* 1.3 60.7 + - - +
359A ASN* 5.8 0.7 - - + -
364A TYR* 4.2 12.7 - - + -
365A SER 3.2 6.1 - - - +
366A LEU* 3.5 17.3 - - + -
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Residues in contact with ILE 358 (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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7A ARG* 3.8 20.6 - - - +
9A GLU* 4.2 13.9 - - + +
13A ARG* 3.4 25.2 + - - +
338A GLU* 3.3 36.1 - - + +
339A ASN 3.3 4.7 - - - +
356A HIS* 3.8 10.8 - - + -
357A GLU* 1.3 80.1 - - - +
359A ASN* 1.3 60.7 + - - +
364A TYR* 3.3 5.4 - - - +
365A SER* 2.9 45.1 + - - +
367A VAL* 3.9 17.5 - - + -
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Residues in contact with ASN 359 (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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13A ARG* 4.1 0.2 - - - -
312A TRP 5.3 1.0 - - - +
313A LEU* 4.4 8.7 - - - +
338A GLU* 5.9 0.4 - - - +
339A ASN* 2.9 59.0 + - + +
340A SER* 5.8 0.2 - - - -
341A ALA 6.2 0.4 - - - +
357A GLU* 5.8 0.7 - - + -
358A ILE* 1.3 74.1 - - - +
360A SER* 1.3 65.3 + - - +
361A ASN 3.5 1.2 - - - +
362A GLU* 2.7 54.3 - - - +
363A VAL 3.4 5.4 - - - +
364A TYR* 3.4 33.2 + - + -
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Residues in contact with SER 360 (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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13A ARG* 3.5 23.5 + - - +
339A ASN* 4.8 1.3 - - - +
359A ASN* 1.3 75.2 + - - +
361A ASN* 1.3 84.0 + - - +
362A GLU 3.3 1.1 - - - -
363A VAL* 3.0 26.4 + - - +
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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