Contacts of the helix formed by residues 320 - 328 (chain D) in PDB entry 1KHU
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 ASN 320 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279D LEU* 4.8 8.8 - - - +
318D ASN 4.8 3.9 - - - +
319D ARG* 1.3 77.0 - - - +
321D SER* 1.3 64.7 + - - +
322D THR* 3.2 20.3 - - + +
323D ILE* 2.9 35.3 + - - +
324D GLU* 2.9 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 321 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320D ASN* 1.3 73.9 - - - +
322D THR* 1.3 68.4 + - - +
324D GLU* 3.1 8.2 + - - +
325D ASN* 2.8 31.1 + - - +
328D ARG* 5.3 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 322 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320D ASN* 3.2 25.1 + - - +
321D SER* 1.3 80.6 + - - +
323D ILE* 1.3 59.1 + - + +
325D ASN* 3.5 7.9 + - - +
326D THR* 3.2 24.6 + - - -
418D LYS* 5.5 2.6 - - - -
426D ARG* 4.4 15.1 + - - -
433D PRO* 4.3 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 323 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278D GLU* 3.4 41.7 - - + +
279D LEU* 4.0 25.4 - - + -
316D ASN* 4.6 0.9 - - - +
318D ASN 4.5 4.0 - - - +
319D ARG* 3.8 14.8 - - + -
320D ASN* 2.9 39.8 - - - +
322D THR* 1.3 74.3 - - - +
324D GLU* 1.3 63.2 + - - +
325D ASN 3.1 0.2 - - - -
326D THR* 3.2 2.3 + - - -
327D ARG* 2.8 33.2 + - - +
433D PRO* 3.6 31.6 - - + +
434D CYS* 4.2 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 324 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319D ARG* 3.6 20.1 + - + +
320D ASN 2.9 13.5 + - - +
321D SER* 3.7 10.1 - - - +
323D ILE* 1.3 77.2 - - - +
325D ASN* 1.3 63.9 + - - +
327D ARG* 3.3 31.7 + - - +
328D ARG* 3.1 57.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 325 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461C ILE* 3.9 20.6 - - - +
321D SER 2.8 16.3 + - - +
322D THR* 3.7 9.4 - - - +
324D GLU* 1.3 77.8 - - - +
326D THR* 1.3 63.9 + - - +
328D ARG* 3.1 25.8 + - - +
329D HIS* 3.1 37.3 + - - -
418D LYS* 5.7 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 326 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461C ILE* 5.7 2.0 - - - +
322D THR 3.2 11.9 + - - -
323D ILE 3.2 6.9 + - - -
325D ASN* 1.3 78.7 + - - +
327D ARG* 1.3 64.4 + - - +
329D HIS* 3.0 17.3 + - - +
330D ILE* 3.5 9.4 + - - +
416D PHE* 3.7 10.8 - - + +
417D VAL* 3.6 33.0 - - + -
418D LYS* 3.7 15.2 - - + -
433D PRO* 3.3 25.6 - - + +
434D CYS* 4.2 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 327 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276D TYR* 3.5 15.9 + - - +
278D GLU* 3.2 17.7 + - - -
298D GLY* 5.1 7.1 - - - +
311D LEU* 3.4 21.6 + - - +
312D GLY* 3.1 29.9 + - - -
314D LEU* 3.4 6.1 + - - +
319D ARG* 3.2 45.8 - - - +
323D ILE* 2.8 20.3 + - - +
324D GLU* 3.4 23.7 + - - +
325D ASN 3.2 0.2 - - - -
326D THR* 1.3 75.8 - - - +
328D ARG* 1.3 62.5 + - - +
329D HIS 3.1 1.0 + - - -
330D ILE* 3.3 24.4 + - + +
331D GLY 4.7 1.0 + - - -
434D CYS* 3.4 17.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 328 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321D SER 5.3 0.4 + - - -
324D GLU* 3.1 48.8 + - + +
325D ASN* 3.1 24.7 + - - +
327D ARG* 1.3 76.4 - - + +
329D HIS* 1.3 68.6 + - + +
330D ILE 3.6 0.6 + - - -
331D GLY* 4.7 3.9 + - - -
----------------------------------------------------------
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