Contacts of the helix formed by residues 318 - 333 (chain A) in PDB entry 4WMJ
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 318 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ARG* 4.3 4.0 - - - +
309A HIS* 3.8 5.2 + - - -
310A PHE* 2.9 38.2 + - - +
313A ALA* 3.1 18.6 + - - +
314A PRO 3.2 13.2 - - - +
315A LEU* 3.3 14.9 + - - +
316A GLU 3.7 0.4 - - - -
317A LYS* 1.4 74.2 - - - +
319A ALA* 1.3 63.0 + - - +
320A PRO* 3.1 19.0 - - - +
321A VAL* 3.1 22.7 + - + +
322A ILE* 3.0 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LEU* 3.7 16.6 - - + +
47A ILE* 4.1 11.9 - - + -
57A LEU* 4.1 19.5 - - + +
306A MET* 5.1 0.4 - - - -
309A HIS* 3.0 19.4 + - + +
318A ASN* 1.3 70.5 - - - +
320A PRO* 1.3 72.9 - - + +
322A ILE* 3.2 3.0 + - - +
323A LEU* 3.0 29.0 + - - +
496A MET* 4.2 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A MET* 4.4 6.3 - - - -
309A HIS* 3.8 11.7 - - + -
310A PHE* 4.0 13.5 - - + -
318A ASN* 3.1 11.7 - - - +
319A ALA* 1.3 94.6 - - + +
321A VAL* 1.3 60.8 + - - +
323A LEU* 3.5 1.4 + - + +
324A ALA* 3.0 24.7 + - - +
496A MET* 3.6 28.3 - - + +
499A HIS* 3.6 31.4 - - + +
500A LYS* 3.6 17.3 - - + +
503A THR* 4.9 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ALA* 4.3 7.9 - - + -
81A VAL* 4.3 6.5 - - + -
85A ARG* 6.3 0.2 - - - +
310A PHE* 4.0 16.6 - - + -
315A LEU* 4.0 36.6 - - + +
318A ASN* 3.1 32.3 + - + +
320A PRO* 1.3 76.3 - - - +
322A ILE* 1.3 59.1 + - - +
324A ALA* 3.2 6.3 + - - +
325A LEU* 2.9 49.8 + - + +
503A THR* 4.2 11.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LEU* 4.6 6.5 - - + -
57A LEU* 4.7 4.3 - - + -
59A TYR* 3.8 54.7 - - + +
69A PHE* 4.4 14.4 - - + -
73A LEU* 5.4 1.6 - - + -
315A LEU 3.8 9.9 - - - +
316A GLU 3.7 22.7 - - - +
317A LYS* 4.3 2.5 - - - -
318A ASN 3.0 26.3 + - - +
319A ALA* 3.8 4.3 - - - +
321A VAL* 1.3 77.4 - - + +
323A LEU* 1.3 64.3 + - - +
325A LEU* 3.3 7.4 + - + +
326A LEU* 3.0 31.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 323 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LEU* 4.0 26.9 - - + -
319A ALA 3.0 18.5 + - - +
320A PRO* 3.8 4.7 - - + +
322A ILE* 1.3 80.3 - - - +
324A ALA* 1.3 61.1 + - - +
326A LEU* 3.4 7.5 + - + +
327A GLY 3.1 17.3 + - - -
408A ASP* 4.8 6.7 - - - +
478A ASN* 3.5 28.0 - - + +
480A ILE* 5.1 1.6 - - + -
496A MET* 3.7 42.4 - - + -
497A TYR* 4.5 15.9 - - + -
500A LYS* 3.8 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A PRO 3.0 19.0 + - - +
321A VAL 3.5 1.3 - - - +
323A LEU* 1.3 74.7 - - - +
325A LEU* 1.3 57.9 + - - +
327A GLY 3.2 0.3 + - - -
328A VAL* 3.0 30.6 + - - +
500A LYS* 3.5 20.8 - - - +
503A THR* 3.4 30.5 - - + -
504A GLN* 3.1 23.0 + - + +
507A ILE* 5.1 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A PHE* 6.0 2.2 - - + -
72A LEU* 3.4 58.9 - - + +
73A LEU* 3.8 18.6 - - + +
75A LEU* 4.6 6.7 - - + -
76A ALA* 4.2 11.9 - - + +
321A VAL* 2.9 36.8 + - + +
322A ILE* 3.7 7.2 - - + +
324A ALA* 1.3 74.4 - - + +
326A LEU* 1.3 59.9 + - + +
328A VAL* 3.2 6.2 + - + +
329A TRP* 3.0 26.9 + - - +
507A ILE* 3.8 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A TYR* 3.9 13.0 - - + -
62A ASN* 3.8 29.6 - - + +
64A ILE* 3.9 25.8 - - + -
69A PHE* 6.4 0.4 - - + -
72A LEU* 5.0 4.9 - - + -
322A ILE* 3.0 31.4 + - + +
323A LEU* 3.7 7.0 - - + +
325A LEU* 1.3 75.2 - - + +
327A GLY* 1.3 64.0 + - - +
329A TRP* 3.1 7.0 + - + +
330A TYR* 3.0 41.4 + - + -
478A ASN* 3.7 33.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A LEU 3.1 12.9 + - - -
324A ALA 3.2 0.6 + - - -
326A LEU* 1.3 77.6 - - - +
328A VAL* 1.3 56.8 + - - +
330A TYR* 4.2 5.6 - - - +
331A GLY* 2.9 25.6 + - - -
332A ASN* 5.0 0.2 + - - -
339A HIS* 5.8 5.8 - - - -
406A PRO* 6.5 0.2 - - - -
500A LYS* 5.2 4.0 - - - -
504A GLN* 3.6 19.7 - - - -
508A TRP* 5.2 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A TYR* 5.0 2.5 - - + -
72A LEU* 5.3 2.7 - - + -
75A LEU* 4.1 25.1 - - + -
324A ALA 3.0 17.4 + - - +
325A LEU* 3.2 10.7 + - + +
327A GLY* 1.3 74.3 - - - +
329A TRP* 1.3 60.8 + - - +
332A ASN* 2.7 51.5 + - + +
333A PHE* 3.7 9.5 + - + -
504A GLN* 4.3 6.7 - - + +
507A ILE* 4.3 24.0 - - + -
508A TRP* 4.1 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 3.9 28.9 - - + -
19A TYR* 3.7 26.2 - + - -
20A TYR* 3.9 21.5 - + + -
27A ILE* 4.2 11.0 - - + -
63A ARG 2.9 22.6 + - - -
64A ILE* 4.3 12.3 - - + -
68A THR* 3.6 17.4 - - + +
72A LEU* 4.1 11.9 - - + +
325A LEU 3.0 13.8 + - - +
326A LEU* 3.1 12.5 + - + +
328A VAL* 1.3 77.1 - - - +
330A TYR* 1.3 80.0 + + - +
333A PHE* 3.2 53.2 + + + +
334A TYR* 3.2 30.7 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ASN* 2.6 33.0 + - - +
63A ARG* 2.8 39.6 + - + -
326A LEU* 3.0 34.7 + - + +
327A GLY* 4.4 4.3 - - - +
329A TRP* 1.3 91.6 - + - +
331A GLY* 1.3 58.1 + - - +
334A TYR* 3.3 21.1 - + - +
335A GLY 2.9 11.3 + - - -
336A ALA* 2.9 28.1 + - + -
404A LEU* 4.1 10.3 - - + -
406A PRO* 3.5 35.0 - - + -
476A PRO* 3.2 21.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A GLY 2.9 18.5 + - - -
330A TYR* 1.3 77.1 - - - +
332A ASN* 1.3 61.2 + - - +
335A GLY* 3.3 22.3 - - - -
336A ALA* 3.5 17.5 - - - +
377A SER* 4.1 14.9 + - - -
378A THR 6.0 0.2 - - - -
508A TRP* 6.2 1.1 - - - -
403B ARG* 5.1 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A TYR* 3.3 31.1 + - + +
17A GLN* 5.0 3.5 + - - -
328A VAL* 2.7 32.4 + - - +
331A GLY* 1.3 75.0 - - - -
333A PHE* 1.3 71.4 + - + +
335A GLY* 4.5 1.0 + - - -
376A TYR* 3.9 5.9 - - - +
377A SER* 2.8 33.9 + - - +
508A TRP* 2.9 38.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A TYR* 3.5 43.7 - + - -
16A LEU* 3.5 32.1 - - + -
17A GLN* 3.4 55.5 - - - +
20A TYR* 3.3 39.1 + - + -
72A LEU* 5.7 0.2 - - + -
328A VAL* 3.8 18.2 - - + -
329A TRP* 3.2 27.2 + + + +
332A ASN* 1.3 82.5 - - + +
334A TYR* 1.3 63.2 + - - +
335A GLY* 3.3 2.2 + - - -
----------------------------------------------------------
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