Contacts of the helix formed by residues 52 - 68 (chain A) in PDB entry 1H3F
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 HIS 52 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ASP 5.0 2.5 - - - -
51A LEU* 1.3 74.1 - - - +
53A LEU* 1.3 67.4 + - - +
54A GLY* 2.8 37.7 + - - -
55A HIS* 2.9 50.5 + + - +
56A ALA 3.5 3.1 + - - -
233A MET* 3.5 28.9 + - + -
234A SER* 3.8 0.4 - - - -
235A LYS* 4.4 4.3 - - + -
240A TYR* 4.0 22.4 - + + -
241A ILE 3.1 22.4 - - - +
242A GLY* 3.9 2.2 - - - -
243A LEU* 3.5 8.6 - - - +
502A SO4 2.8 34.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A HIS* 1.3 71.9 - - - +
54A GLY* 1.3 62.6 + - - +
56A ALA* 3.0 18.7 + - + +
57A VAL* 3.6 3.5 + - - +
224A LEU* 3.8 14.6 - - + -
233A MET* 4.0 5.1 - - + -
241A ILE* 3.0 41.2 + - + +
243A LEU* 3.6 12.5 - - + +
250A MET* 5.0 4.5 - - + -
254A LEU* 4.0 22.7 - - + -
265A TYR* 4.8 4.0 - - + -
269A LEU* 3.6 36.0 - - + +
296A LEU* 4.3 6.3 - - + -
300A TYR* 3.8 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A HIS* 2.8 22.6 + - - -
53A LEU* 1.3 78.8 - - - +
55A HIS* 1.3 60.7 + - - +
56A ALA 3.3 0.3 + - - -
57A VAL* 3.4 17.8 + - - +
58A VAL* 4.6 1.4 + - - +
224A LEU* 3.9 23.4 + - - +
233A MET* 3.6 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ARG* 5.1 6.3 + - - +
50A ASP 3.9 13.5 - - - -
51A LEU* 3.5 25.9 - - + +
52A HIS* 2.9 60.4 + + - +
54A GLY* 1.3 76.5 - - - +
56A ALA* 1.3 61.4 + - - +
57A VAL 3.2 0.6 + - - -
58A VAL* 3.6 5.6 + - - +
59A LEU* 3.2 33.7 + - + +
108A TYR* 5.5 4.5 - + - +
243A LEU* 5.7 0.2 - - + -
502A SO4 3.7 23.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A HIS 3.5 2.7 + - - +
53A LEU* 3.0 23.3 + - + +
55A HIS* 1.3 77.7 - - - +
57A VAL* 1.3 64.6 + - - +
59A LEU* 3.8 0.7 - - - -
60A ARG* 2.9 30.1 + - + +
115A ILE* 3.8 17.9 - - + -
243A LEU* 4.6 2.4 - - + +
268A LEU 5.1 1.1 - - - -
269A LEU* 4.5 8.3 - - + -
300A TYR* 3.5 26.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LEU 4.0 7.9 - - - +
54A GLY 3.5 15.5 - - - +
55A HIS 3.2 1.0 - - - -
56A ALA* 1.3 79.0 - - - +
58A VAL* 1.3 64.0 + - + +
60A ARG* 4.3 2.3 - - - +
61A LYS* 3.6 16.1 + - - +
221A MET* 3.9 28.9 - - + +
222A PRO 3.7 21.8 - - - +
224A LEU* 4.2 17.0 - - + +
268A LEU* 4.0 43.9 - - + +
269A LEU* 4.2 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 4.0 16.8 - - + -
54A GLY 4.6 0.4 + - - -
55A HIS* 3.6 6.7 + - - +
56A ALA 3.4 0.2 - - - -
57A VAL* 1.3 78.2 - - + +
59A LEU* 1.3 66.6 + - + +
61A LYS* 3.1 6.4 + - - +
62A MET* 3.1 39.1 + - - +
192A MET* 3.9 17.7 - - + +
193A GLY* 4.0 22.2 - - - +
194A GLY* 4.3 4.5 - - - +
221A MET* 3.9 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 3.7 29.4 - - + -
51A LEU* 4.0 27.6 - - + -
55A HIS* 3.2 29.6 + - + +
56A ALA 4.2 0.2 - - - +
58A VAL* 1.3 78.3 - - + +
60A ARG* 1.3 56.6 + - - +
62A MET* 3.1 9.7 + - - +
63A ARG 2.9 22.0 + - - -
74A LEU* 5.5 0.4 - - + -
108A TYR* 4.3 10.1 - - - +
112A ALA* 4.9 7.4 - - + -
115A ILE* 3.5 29.3 - - + +
116A LEU* 3.5 31.4 - - + +
243A LEU* 5.3 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ALA* 2.9 23.4 + - - +
57A VAL 4.3 2.2 - - - +
59A LEU* 1.3 73.5 - - - +
61A LYS* 1.3 65.5 + - - +
63A ARG* 3.2 5.8 + - - +
64A GLN* 3.0 21.1 + - - +
115A ILE* 3.8 18.6 - - + -
268A LEU 4.4 5.7 + - - +
269A LEU* 3.4 36.2 + - - +
270A THR 3.9 4.0 + - - +
271A ASP* 2.5 42.6 + - - -
300A TYR* 3.7 20.6 - - - +
305A ILE* 3.8 13.9 - - + +
306A PRO 5.4 0.2 + - - -
307A PRO 4.3 9.7 + - - -
308A ARG* 4.5 0.2 - - - +
309A ILE* 3.8 21.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU 3.6 3.6 + - - -
15A LEU* 2.9 27.8 + - + +
17A ARG* 2.9 27.3 + - - +
19A ALA 5.1 0.2 - - - +
57A VAL 3.6 11.7 + - - +
58A VAL 3.1 10.4 + - - +
60A ARG* 1.3 78.6 - - - +
62A MET* 1.3 62.7 + - - +
64A GLN* 2.7 35.8 + - - +
65A PHE* 3.1 21.8 + - + -
192A MET* 3.7 24.0 - - + -
219A PHE* 3.8 15.7 - - + -
221A MET* 4.0 20.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A VAL* 4.5 6.5 - - + +
42A LEU* 3.4 48.9 - - + +
58A VAL* 3.1 23.8 + - - +
59A LEU* 3.3 11.4 - - - +
61A LYS* 1.3 74.7 - - - +
63A ARG* 1.3 64.5 + - - +
65A PHE* 3.1 11.2 + - - +
66A GLN* 3.0 26.5 + - - +
72A VAL* 3.4 36.1 - - + +
74A LEU* 5.2 1.1 - - + -
116A LEU* 3.7 17.9 - - + -
192A MET* 3.6 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A LEU 2.9 11.6 + - - +
60A ARG* 3.2 14.6 + - + +
62A MET* 1.3 75.4 - - - +
64A GLN* 1.3 57.6 + - - +
66A GLN* 3.2 20.7 + - - +
67A GLU* 2.7 57.6 + - + +
115A ILE* 3.0 34.8 + - + +
116A LEU* 4.1 0.8 - - - +
117A ARG* 3.5 17.2 - - - +
304A GLN* 4.0 14.6 + - - +
305A ILE* 3.0 41.0 + - + +
306A PRO 4.0 0.4 + - - -
307A PRO* 3.7 30.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 3.4 42.2 + - + +
15A LEU* 3.8 10.5 - - + -
17A ARG* 6.0 0.2 - - - +
60A ARG 3.0 12.6 + - - +
61A LYS* 2.7 44.0 + - - +
62A MET 3.1 0.4 - - - -
63A ARG* 1.3 75.1 - - - +
65A PHE* 1.3 66.0 + - - +
67A GLU* 3.2 8.6 + - + +
68A LEU* 3.1 30.6 + - + +
271A ASP* 5.8 1.8 + - - -
307A PRO 6.0 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 3.4 33.4 - - + -
28A LEU* 4.7 8.1 - - + -
32A LEU* 5.0 3.1 - - + -
38A LEU* 5.0 2.0 - - + -
40A VAL* 3.9 34.8 - - + -
61A LYS* 3.1 23.1 + - + -
62A MET* 3.4 12.3 - - - +
64A GLN* 1.3 74.8 - - - +
66A GLN* 1.3 61.9 + - + +
68A LEU* 3.1 9.8 + - - -
69A GLY 3.3 0.3 + - - -
70A HIS* 2.9 50.0 + + + +
72A VAL* 5.3 1.3 - - + -
190A VAL* 4.3 18.2 - - + -
192A MET* 4.0 17.5 - - - -
219A PHE* 3.9 29.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A MET 3.0 14.7 + - - +
63A ARG* 3.2 20.3 + - - +
65A PHE* 1.3 72.3 - - - +
67A GLU* 1.3 56.6 + - - +
68A LEU 3.0 4.7 - - - -
69A GLY* 2.8 21.7 + - - -
70A HIS 3.4 11.4 - - - +
72A VAL* 3.7 26.4 - - + +
116A LEU* 3.5 10.7 - - - +
117A ARG* 2.8 50.9 + - + +
122A LEU* 2.9 49.8 + - + +
123A PHE* 3.9 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A HIS* 6.2 0.2 - - - -
63A ARG* 2.7 51.1 + - + +
64A GLN* 3.2 8.9 + - + +
66A GLN* 1.3 74.6 - - - +
68A LEU* 1.3 61.7 + - + +
69A GLY 3.2 1.2 + - - -
117A ARG* 3.0 32.5 + - - +
307A PRO* 3.7 32.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A HIS* 3.9 41.5 - - + +
11A ALA* 4.1 22.9 - - + +
14A LEU* 4.7 9.6 - - + -
15A LEU* 4.0 33.2 - - + -
64A GLN* 3.1 22.2 + - + +
65A PHE* 3.4 9.2 - - - +
66A GLN 3.0 1.2 - - - -
67A GLU* 1.3 79.4 - - + +
69A GLY* 1.3 59.7 + - - +
70A HIS* 3.5 21.1 + - + +
----------------------------------------------------------
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