Contacts of the strand formed by residues 351 - 358 (chain B) in PDB entry 3S95
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 GLY 351 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B STU 5.0 4.7 - - - +
346B GLY 4.6 0.2 - - - +
348B GLY* 3.0 24.8 + - - -
350B PHE* 1.3 81.2 - - - +
352B GLN* 1.3 59.9 + - - -
368B LYS* 4.7 16.6 - - - +
369B GLU 3.3 14.1 - - - -
370B LEU* 4.1 6.2 - - - +
371B ILE* 3.9 9.6 - - - -
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Residues in contact with GLN 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B STU 5.2 1.8 - - - -
344B VAL* 3.9 21.0 - - + +
346B GLY 3.4 13.2 - - - +
347B LYS* 4.0 7.3 - - + +
351B GLY* 1.3 73.7 - - - +
353B ALA* 1.3 59.2 + - - +
354B ILE* 3.5 20.2 - - + +
367B MET 3.6 1.2 - - - +
368B LYS* 3.3 9.1 - - - +
369B GLU* 2.8 68.1 + - + +
371B ILE* 3.9 24.7 - - + +
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Residues in contact with ALA 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B STU 3.6 53.3 - - + +
344B VAL* 3.6 3.3 - - - +
345B LEU* 2.7 35.1 + - + -
346B GLY 2.9 11.5 + - - +
352B GLN* 1.3 71.9 - - - +
354B ILE* 1.3 56.7 + - - +
366B VAL* 3.9 10.8 - - + -
367B MET 3.4 5.4 - - - -
368B LYS* 4.6 2.0 - - + +
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Residues in contact with ILE 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341B HIS* 4.6 12.6 - - + -
342B GLY 3.6 20.0 - - - +
343B GLU 3.6 3.8 - - - +
344B VAL* 4.3 11.0 - - + +
345B LEU* 4.4 0.2 - - - -
352B GLN* 3.5 22.9 - - + +
353B ALA* 1.3 77.8 - - - +
355B LYS* 1.3 77.5 + - - +
356B VAL* 3.4 7.8 + - + +
366B VAL* 3.4 4.8 - - - -
367B MET* 2.8 62.8 + - + +
369B GLU* 3.3 28.9 - - + +
405B LYS* 5.2 0.2 - - - +
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Residues in contact with LYS 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342B GLY* 2.7 34.4 + - - -
343B GLU* 2.8 45.2 + - + +
345B LEU* 3.9 16.2 - - + +
354B ILE* 1.3 75.7 - - - +
356B VAL* 1.3 57.5 + - - +
357B THR* 4.8 6.7 - - - +
364B VAL* 3.6 29.3 - - + +
365B MET 3.6 6.3 - - - +
415B TYR* 3.8 39.6 + - + +
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Residues in contact with VAL 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339B LEU* 4.1 33.9 - - + -
340B ILE 3.4 9.6 - - - +
341B HIS* 4.3 13.9 - - + -
354B ILE* 3.4 15.4 + - + +
355B LYS* 1.3 80.0 - - - +
357B THR* 1.3 62.7 + - - +
358B HIS 4.3 0.2 - - - -
363B GLU 3.8 0.2 - - - +
364B VAL* 3.4 4.7 - - - +
365B MET* 2.8 57.5 + - + +
366B VAL 4.0 3.8 - - - +
367B MET* 4.0 23.1 - - + +
412B ILE* 4.4 3.4 - - + -
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Residues in contact with THR 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339B LEU* 3.4 4.3 - - - -
340B ILE* 2.8 56.7 + - + +
355B LYS* 4.8 6.1 - - - -
356B VAL* 1.3 79.1 + - - +
358B HIS* 1.3 73.8 + - - +
359B ARG 3.4 0.5 + - - -
362B GLY* 3.9 15.5 - - - +
363B GLU 3.3 9.2 - - - +
364B VAL* 3.7 17.9 - - + +
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Residues in contact with HIS 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332B ARG* 5.1 0.9 + - - -
334B PHE* 3.8 32.6 - + - -
338B ASP* 3.5 28.8 + - + +
339B LEU* 4.0 7.7 - - + +
357B THR* 1.3 75.4 - - - +
359B ARG* 1.3 59.8 + - - +
360B GLU* 3.0 47.2 + - + -
361B THR* 3.2 33.1 + - + +
362B GLY* 2.9 28.2 + - - -
363B GLU* 2.8 18.8 + - + +
365B MET* 4.2 8.9 - - + +
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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