Contacts of the helix formed by residues 301 - 318 (chain D) in PDB entry 1SZU
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 301 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C GLY 4.1 6.1 + - - -
274C PHE* 4.7 0.6 - - - +
275C PRO* 3.8 27.5 - - + +
74D SER* 3.0 24.5 + - - -
75D HIS* 4.8 5.2 + - - +
83D TYR* 4.3 0.2 - - - -
109D THR* 6.0 0.4 - - + -
275D PRO 4.4 3.3 + - - +
276D LEU* 4.2 4.4 - - - +
298D TYR* 3.1 17.8 + - - +
300D GLY* 1.3 74.0 - - - +
302D PRO* 1.3 59.1 - - - +
303D ILE* 3.1 10.5 + - - +
304D ALA* 2.9 27.9 + - + +
305D CYS* 2.8 32.9 + - - -
1026D EDO 2.8 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 302 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D GLN* 3.9 10.8 - - - +
73D LEU* 3.5 37.7 - - + +
74D SER 3.3 25.1 - - - +
75D HIS* 4.0 8.3 - - + +
76D THR 5.3 0.2 - - - +
83D TYR* 3.7 33.9 - - + +
85D PRO* 4.4 2.1 - - + +
300D GLY 3.6 5.4 - - - +
301D ASN* 1.3 83.0 - - - +
303D ILE* 1.3 63.1 + - - +
305D CYS* 3.1 14.2 + - + +
306D VAL* 3.2 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 303 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C PHE* 4.8 3.6 - - + -
303C ILE* 6.3 0.9 - - + -
66D VAL* 3.5 32.5 - - + +
69D GLN* 4.0 13.2 - - + -
70D LEU* 4.2 22.7 - - + -
73D LEU 3.5 9.9 - - - +
74D SER* 3.3 40.4 - - - +
274D PHE* 4.0 11.0 - - + -
301D ASN* 3.1 8.7 + - - +
302D PRO* 1.3 79.2 - - - +
304D ALA* 1.3 63.5 + - - +
306D VAL* 3.3 6.8 - - - +
307D ALA* 3.2 19.8 + - - +
1026D EDO 3.6 20.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 304 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271D ALA* 3.8 4.0 - - - +
274D PHE* 3.9 17.5 - - + -
275D PRO 3.2 28.7 - - - +
276D LEU* 3.8 14.8 - - + +
301D ASN* 2.9 20.4 + - + +
303D ILE* 1.3 77.3 - - - +
305D CYS* 1.3 58.2 + - - +
307D ALA* 3.4 2.6 + - - +
308D ALA* 2.9 27.7 + - - +
1026D EDO 3.9 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 305 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D TYR* 4.6 0.4 - - - -
85D PRO* 3.7 22.2 - - + +
86D TYR* 3.8 23.6 - - - -
89D LEU* 4.4 3.9 - - + +
107D LEU* 4.0 13.7 - - - -
276D LEU* 4.4 5.4 - - - -
300D GLY* 3.6 22.4 - - - -
301D ASN 2.8 25.4 + - - -
302D PRO 3.1 7.4 + - - +
304D ALA* 1.3 70.8 - - - +
306D VAL* 1.3 66.4 + - - +
308D ALA* 3.0 8.2 + - - +
309D LEU* 2.8 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 306 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D ALA* 3.6 37.1 - - + +
66D VAL* 4.0 4.0 - - - +
69D GLN* 3.7 33.7 - - + +
85D PRO* 3.9 17.7 - - + -
302D PRO 3.2 8.2 + - - +
303D ILE 3.3 12.1 - - - +
305D CYS* 1.3 75.5 - - - +
307D ALA* 1.3 60.3 + - - +
309D LEU* 3.4 12.5 + - + +
310D GLU* 2.9 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 307 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D VAL* 3.8 21.6 - - + +
66D VAL* 3.9 7.0 - - + -
271D ALA 3.6 17.7 - - - +
274D PHE* 3.8 12.6 - - + -
303D ILE 3.2 9.6 + - - +
304D ALA* 3.4 10.5 - - - +
306D VAL* 1.3 83.6 - - - +
308D ALA* 1.3 55.9 + - - +
310D GLU* 3.1 5.6 + - - +
311D VAL* 2.8 34.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 308 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89D LEU* 3.9 15.5 - - + -
270D ILE* 3.3 26.8 - - + +
271D ALA* 4.0 2.4 - - - +
276D LEU* 3.7 21.3 - - + -
304D ALA 2.9 14.7 + - - +
305D CYS 3.0 7.6 + - - +
307D ALA* 1.3 73.0 - - - +
309D LEU* 1.3 63.9 + - - +
311D VAL* 3.2 2.6 + - - +
312D LEU* 3.0 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 309 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D PRO* 4.0 24.2 - - + +
88D GLU* 3.9 26.7 - - + +
89D LEU* 3.7 29.6 - - + +
92D ILE* 3.4 33.0 - - + +
305D CYS 2.8 21.4 + - - +
306D VAL* 3.7 13.2 - - + +
308D ALA* 1.3 72.7 - - - +
310D GLU* 1.3 61.3 + - - +
312D LEU* 3.5 7.5 + - + +
313D LYS* 3.2 34.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 310 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D LYS* 3.3 53.2 - - + +
62D VAL* 3.7 8.5 - - + +
65D ALA* 3.9 16.9 - - + +
306D VAL 2.9 16.7 + - - +
307D ALA 3.5 4.9 - - - +
309D LEU* 1.3 76.2 - - - +
311D VAL* 1.3 65.2 + - - +
312D LEU 3.2 0.2 - - - -
313D LYS* 3.2 37.4 + - - +
314D VAL* 2.9 29.7 + - - +
317D GLN* 4.6 4.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 311 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D THR* 4.0 9.6 - - + +
62D VAL* 4.0 16.8 - - + -
245D ALA* 5.8 1.1 - - + -
269D SER 3.7 9.2 - - - +
270D ILE* 3.4 27.8 - - + +
271D ALA 3.8 1.8 - - - -
272D GLY* 3.7 22.7 - - - +
307D ALA 2.8 18.5 + - - +
308D ALA 3.2 2.4 + - - +
310D GLU* 1.3 75.8 - - - +
312D LEU* 1.3 69.2 + - + +
314D VAL* 3.3 7.9 + - - +
315D PHE* 3.0 53.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 312 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89D LEU* 4.0 21.3 - - + -
92D ILE* 3.8 28.9 - - + -
93D MET* 4.2 9.0 - - - -
96D LYS* 4.5 18.1 + - + +
251D LEU* 4.4 32.1 - - + -
270D ILE* 4.4 16.4 - - + -
308D ALA 3.0 15.8 + - - +
309D LEU* 3.6 11.0 - - + +
310D GLU 3.2 0.2 - - - -
311D VAL* 1.3 81.0 - - + +
313D LYS* 1.3 61.7 + - + +
315D PHE* 3.2 16.9 + - + +
316D GLU* 3.4 15.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 313 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D GLU* 5.8 4.9 - - - -
309D LEU* 3.2 21.2 + - - +
310D GLU* 3.2 34.9 + - - +
312D LEU* 1.3 76.0 - - + +
314D VAL* 1.3 58.6 + - - +
316D GLU* 3.1 7.5 + - - +
317D GLN* 2.9 52.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 314 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D THR* 4.1 7.0 - - + -
59D HIS* 3.4 46.7 - - + +
61D LYS* 3.8 18.6 - - + -
62D VAL* 4.8 2.5 - - + -
310D GLU* 2.9 24.2 + - + +
311D VAL* 3.5 7.6 - - - +
313D LYS* 1.3 76.1 - - + +
315D PHE* 1.3 59.0 + - - +
317D GLN* 4.5 8.1 - - - +
318D GLU* 2.8 41.1 + - - +
320D LEU* 3.9 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 315 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D ASN* 4.1 9.2 - - + -
55D THR* 3.8 15.0 - - + -
96D LYS* 6.2 0.4 - - - +
245D ALA* 3.0 31.9 - - + -
246D GLY* 3.8 14.4 - - - -
251D LEU* 4.9 12.8 - - + -
269D SER 5.3 0.2 - - - -
311D VAL* 3.0 45.8 + - + -
312D LEU* 3.5 12.6 - - + +
313D LYS 3.2 0.2 - - - -
314D VAL* 1.3 75.9 - - - +
316D GLU* 1.3 65.1 + - - +
319D ASN* 3.4 3.3 + - - -
320D LEU* 3.3 50.1 + - + +
321D LEU* 3.8 26.3 + - + +
403D LEU* 3.9 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 316 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D LYS* 4.1 21.0 + - - +
312D LEU 3.4 10.9 + - - +
313D LYS* 3.1 10.1 + - - +
315D PHE* 1.3 81.5 - - - +
317D GLN* 1.3 68.1 + - + +
318D GLU 3.3 0.7 + - - -
319D ASN* 3.3 11.3 + - - +
321D LEU* 5.1 11.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 317 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D LYS* 4.7 18.3 + - - +
310D GLU* 4.6 6.1 + - - -
313D LYS* 2.9 52.4 + - - +
314D VAL* 4.2 6.2 - - - +
316D GLU* 1.3 74.8 - - + +
318D GLU* 1.3 67.2 + - + +
319D ASN* 3.8 0.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 318 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D HIS* 2.9 38.8 + - - -
61D LYS* 4.7 5.0 - - - +
314D VAL* 2.8 29.6 + - + +
317D GLN* 1.3 80.8 - - + +
319D ASN* 1.3 69.9 + - - +
320D LEU* 3.3 11.3 + - + +
323D LYS* 2.9 34.4 + - - +
404D THR* 4.4 11.4 - - - +
----------------------------------------------------------
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