Contacts of the helix formed by residues 345 - 353 (chain B) in PDB entry 3N57
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 SER 345 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B LEU 5.5 0.7 - - - -
340B HIS* 3.2 36.9 + - - -
341B GLU* 3.4 8.0 - - - -
342B GLY 2.6 22.8 + - - -
343B PRO 3.3 1.0 + - - -
344B GLY* 1.3 82.8 - - - +
346B LEU* 1.3 64.5 + - - +
348B SER* 3.3 26.7 + - - -
349B GLU* 3.5 4.5 + - - +
397B TYR* 4.3 7.6 - - - -
521B LYS 5.2 0.2 - - - +
522B PHE* 3.9 7.2 - - - -
523B LYS 4.7 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 346 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B ILE* 4.3 25.3 + - + +
345B SER* 1.3 72.7 - - - +
347B LEU* 1.3 64.2 + - - +
348B SER 3.3 0.3 + - - -
349B GLU* 3.3 4.3 + - - +
350B LEU* 3.0 45.0 + - + +
359B LEU* 3.7 21.5 - - + -
375B ILE* 4.5 7.4 - - + -
393B HIS* 3.9 15.7 - - + +
394B MET* 3.8 24.9 - - + +
397B TYR* 4.0 28.2 - - + -
522B PHE* 3.6 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 347 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B HIS 4.2 12.9 + - - +
341B GLU* 3.6 42.4 - - + +
345B SER* 3.3 3.3 + - - +
346B LEU* 1.3 78.4 - - - +
348B SER* 1.3 57.5 + - - +
350B LEU* 3.2 3.8 + - - -
351B LYS* 2.8 44.4 + - + +
356B VAL* 3.6 29.2 - - + -
357B ASN 4.0 9.9 - - - +
358B THR* 3.9 11.0 - - - +
359B LEU* 3.8 30.6 - - + +
605B ASN* 4.5 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 348 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B GLU 3.9 2.2 + - - -
342B GLY 3.2 14.8 + - - -
344B GLY 4.5 4.5 - - - -
345B SER* 3.3 19.1 + - - -
346B LEU 3.2 0.6 - - - -
347B LEU* 1.3 77.8 - - - +
349B GLU* 1.3 57.7 + - - +
351B LYS* 3.3 7.0 + - - +
352B SER* 3.0 31.7 + - - -
606B GLU* 2.4 37.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 349 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B SER 3.5 2.1 + - - +
346B LEU 3.3 1.6 + - - -
347B LEU 3.3 0.2 - - - -
348B SER* 1.3 73.5 - - - +
350B LEU* 1.3 63.1 + - - +
351B LYS 3.0 5.9 + - - -
352B SER* 3.2 7.5 + - - +
353B LYS* 3.1 52.1 + - + +
393B HIS* 3.9 25.9 + - + +
519B ASN* 4.9 3.0 + - - +
521B LYS* 2.8 51.8 + - + +
522B PHE* 3.6 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 350 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B LEU* 3.0 39.4 + - + +
347B LEU 3.2 4.0 + - - +
349B GLU* 1.3 75.0 - - - +
351B LYS* 1.3 56.4 + - - +
353B LYS* 4.1 4.2 + - + -
354B GLY 3.8 0.5 + - - -
355B TRP* 3.1 33.1 + - + +
356B VAL* 3.1 44.4 + - + -
359B LEU* 4.2 18.6 - - + -
377B VAL* 4.5 2.7 - - + -
390B ILE* 4.2 26.9 - - + +
393B HIS* 3.8 29.2 - - + -
394B MET* 5.0 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 351 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B LEU* 2.8 27.6 + - + +
348B SER* 3.5 7.4 - - - +
350B LEU* 1.3 77.6 - - - +
352B SER* 1.3 58.9 + - - +
353B LYS 3.3 0.4 - - - -
354B GLY* 2.9 20.6 + - - -
356B VAL 3.3 18.2 - - - +
357B ASN* 3.9 20.3 + - - +
602B ASP* 3.5 45.5 + - - +
605B ASN* 4.1 21.4 - - - +
606B GLU* 6.4 0.6 - - - +
657B LYS* 5.6 0.2 + - - -
658B ARG* 3.6 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 352 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B SER 3.0 17.8 + - - -
349B GLU* 3.7 15.4 + - - -
351B LYS* 1.3 72.7 - - - +
353B LYS* 1.3 61.2 + - - +
354B GLY 3.0 6.0 + - - -
521B LYS* 5.4 4.9 + - - -
657B LYS* 3.8 12.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 353 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B GLU* 3.1 42.2 + - + +
350B LEU* 4.3 2.5 - - - +
352B SER* 1.3 76.6 - - - +
354B GLY* 1.3 61.7 + - - +
355B TRP* 3.4 62.7 + - + -
382B GLU* 5.4 2.3 - - - +
393B HIS* 4.3 10.6 + - - +
657B LYS* 4.1 8.1 + - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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