Contacts of the helix formed by residues 317 - 325 (chain D) in PDB entry 2NYM
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 CYS 317 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280D LYS* 4.2 30.3 - - - +
313D LEU* 4.9 6.3 - - - -
314D SER* 3.7 29.2 - - - -
315D ALA 3.7 1.4 + - - -
316D ASP* 1.3 76.0 - - - +
318D ARG* 1.3 65.7 + - - +
319D GLU* 3.2 3.1 - - - +
320D ASN* 2.5 39.2 + - - +
321D VAL* 2.7 31.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 318 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310D CYS 3.8 17.7 + - - +
311D GLU* 4.4 15.0 + - - +
313D LEU* 3.9 21.4 + - + -
314D SER 3.3 12.2 + - - +
315D ALA* 4.2 27.6 - - - +
317D CYS* 1.3 85.1 - - - +
319D GLU* 1.3 65.2 + - - +
321D VAL* 3.0 1.9 + - - -
322D ILE* 2.8 42.7 + - + +
355D ILE* 3.2 32.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 319 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317D CYS 3.2 0.8 - - - -
318D ARG* 1.3 82.4 - - - +
320D ASN* 1.3 62.2 + - - +
322D ILE* 3.6 6.0 + - - +
323D MSE 3.2 39.7 + - + +
355D ILE* 3.5 26.1 - - + +
356D LEU* 3.9 17.2 - - + +
360D ASN* 4.9 6.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 320 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280D LYS* 5.1 8.3 - - - +
317D CYS* 2.5 27.3 + - - +
319D GLU* 1.3 76.1 - - - +
321D VAL* 1.3 66.3 + - - +
323D MSE 3.7 3.8 - - - +
324D SER* 2.8 39.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 321 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280D LYS* 5.0 11.9 - - + -
284D VAL* 4.7 7.4 - - + -
313D LEU* 3.7 34.3 - - + -
317D CYS* 2.7 41.8 + - + +
318D ARG 4.0 1.1 - - - +
320D ASN* 1.3 76.7 - - - +
322D ILE* 1.3 66.0 + - - +
323D MSE 2.9 5.8 - - - -
324D SER* 4.2 0.4 - - - -
325D GLN* 2.9 37.2 + - + +
326D ILE* 3.1 19.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 322 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310D CYS* 3.5 35.2 - - + -
313D LEU* 4.1 8.3 - - + -
318D ARG* 2.8 43.0 + - + +
319D GLU 4.1 3.1 - - - +
321D VAL* 1.3 72.7 - - - +
323D MSE 1.3 58.1 + - - +
326D ILE* 4.0 13.2 - - + -
327D LEU* 2.8 28.3 + - + +
352D LEU* 4.0 17.7 - - + -
355D ILE* 3.7 22.0 - - + -
356D LEU* 3.6 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 323 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319D GLU* 3.2 25.5 + - + +
320D ASN* 3.7 4.7 - - - +
321D VAL 2.9 1.6 - - - -
322D ILE* 1.3 81.5 - - - +
324D SER* 1.3 61.5 + - - +
325D GLN 3.5 0.2 - - - -
327D LEU* 3.8 26.2 - - + +
328D PRO* 3.8 5.9 - - - +
356D LEU* 3.8 26.0 - - + -
360D ASN* 3.1 41.7 - - + +
364D HIS* 3.8 27.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 324 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288D GLN* 5.2 0.5 + - - -
320D ASN* 2.8 27.0 + - - -
321D VAL* 4.2 0.2 - - - -
323D MSE 1.3 78.2 - - - +
325D GLN* 1.3 78.6 + - - +
328D PRO* 3.6 15.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 325 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284D VAL* 3.9 24.3 - - + +
285D PRO* 5.7 2.1 - - - +
288D GLN* 2.9 45.5 + - - +
321D VAL* 2.9 24.2 + - + +
324D SER* 1.3 102.3 + - - +
326D ILE* 1.3 62.0 + - + +
328D PRO* 3.7 5.7 - - - +
329D CYS* 3.9 3.1 - - - -
----------------------------------------------------------
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