Contacts of the helix formed by residues 44 - 64 (chain A) in PDB entry 1H4O
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 THR 44 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A GLY* 3.2 17.9 + - - +
42A ALA 3.2 7.2 - - - +
43A PHE* 1.3 79.2 - - - +
45A PRO* 1.3 68.5 - - - +
47A CYS* 2.9 29.3 - - - -
48A SER* 2.6 35.1 + - - -
120A PHE* 3.8 29.4 - - + -
124A ARG* 5.4 0.2 - - - +
1162A BEZ 3.0 13.5 + - - -
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Residues in contact with PRO 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A PHE 4.0 2.2 - - - +
44A THR* 1.3 87.2 - - - +
46A GLY* 1.3 57.3 + - - +
48A SER* 4.6 3.4 - - - -
49A LYS* 2.8 44.5 + - + +
1162A BEZ 3.6 15.0 - - + +
64B ALA 5.2 6.7 - - - +
65B LYS* 6.0 7.9 - - + +
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Residues in contact with GLY 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PRO* 1.3 72.3 - - - +
47A CYS* 1.3 62.2 + - - +
49A LYS* 5.3 0.4 - - - -
50A THR* 3.0 12.6 + - - -
51A HIS* 3.0 20.6 + - - +
127A ARG* 4.4 4.9 - - - -
149A LEU* 4.1 22.8 - - - +
1162A BEZ 2.8 27.1 + - - -
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Residues in contact with CYS 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A VAL* 3.6 9.2 - - + -
40A PRO* 3.5 20.9 - - - -
41A GLY 3.5 19.1 - - - +
44A THR* 2.9 25.8 - - - +
45A PRO 3.3 0.2 - - - -
46A GLY* 1.3 75.7 - - - +
48A SER* 1.3 58.7 + - - +
51A HIS* 3.9 3.1 - - - -
52A LEU* 2.9 36.0 + - - +
84A TRP* 3.7 14.1 - - + -
127A ARG* 3.4 23.8 - - - +
1162A BEZ 3.0 12.7 + - - -
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Residues in contact with SER 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A PHE* 3.4 12.4 - - - -
44A THR 2.6 23.4 + - - -
45A PRO* 3.9 1.8 - - - -
47A CYS* 1.3 77.9 - - - +
49A LYS* 1.3 72.2 + - - +
50A THR 3.5 0.2 - - - -
53A PRO* 3.1 12.9 - - - +
84A TRP* 2.9 22.5 + - - -
88A HIS* 2.8 41.5 - - - -
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Residues in contact with LYS 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PRO* 2.8 28.2 + - + +
46A GLY* 5.3 0.4 - - - -
48A SER* 1.3 85.2 - - - +
50A THR* 1.3 65.5 + - - +
53A PRO* 3.4 14.4 - - - +
88A HIS* 3.5 25.9 + - - -
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Residues in contact with THR 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLY* 3.0 9.9 + - - -
48A SER 3.5 0.2 - - - -
49A LYS* 1.3 86.4 + - - +
51A HIS* 1.3 70.7 + - - +
53A PRO* 3.6 2.2 - - - -
54A GLY* 3.1 21.3 + - - -
149A LEU* 4.0 23.3 - - + +
153A LEU* 4.3 28.1 - - + +
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Residues in contact with HIS 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE* 3.5 24.8 - + - +
38A GLY 3.5 8.5 - - - -
39A VAL* 3.4 9.8 - - + +
46A GLY 3.0 6.0 + - - +
47A CYS* 3.8 7.6 - - - +
50A THR* 1.3 82.2 - - - +
52A LEU* 1.3 66.1 + - - +
54A GLY* 3.4 5.5 + - - -
55A PHE* 3.5 22.4 + + - -
127A ARG* 3.1 56.0 + - + +
128A PHE 3.9 5.4 - - - -
149A LEU* 4.6 0.7 - - + -
152A SER* 2.9 29.9 + - - -
153A LEU* 3.8 17.9 - - + -
154A ALA 5.5 0.5 + - - -
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Residues in contact with LEU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE* 3.9 25.7 - - + -
39A VAL* 5.7 0.2 - - + -
47A CYS 2.9 14.4 + - - +
51A HIS* 1.3 73.5 - - - +
53A PRO* 1.3 73.3 - - + +
55A PHE* 3.0 5.2 + - - -
56A VAL* 3.0 40.0 + - + +
72A CYS* 4.5 0.9 - - + -
84A TRP* 3.7 44.6 - - + +
85A GLY* 4.9 3.1 - - - -
88A HIS* 3.9 24.5 - - + -
90A ALA* 5.0 0.7 - - + -
94A VAL* 4.0 14.6 - - + -
96A LEU* 4.4 15.3 - - + -
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Residues in contact with PRO 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A CYS 3.6 2.7 - - - +
48A SER 3.1 26.9 - - - +
49A LYS* 3.4 21.5 - - - +
50A THR 3.6 3.8 - - - +
51A HIS 3.5 3.1 - - - -
52A LEU* 1.3 98.5 - - + +
54A GLY* 1.3 56.3 + - - +
56A VAL* 3.6 9.7 - - + +
57A GLU* 2.8 46.9 + - - +
88A HIS* 4.5 10.8 - - + +
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Residues in contact with GLY 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A THR 3.1 18.7 + - - -
51A HIS 3.8 1.8 - - - -
52A LEU 3.2 0.4 - - - -
53A PRO* 1.3 77.1 - - - +
55A PHE* 1.3 56.0 + - - +
57A GLU* 3.5 11.2 + - - +
58A GLN* 3.0 35.8 + - - +
154A ALA* 3.8 13.2 - - - -
155A PRO* 5.9 1.8 - - - -
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Residues in contact with PHE 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A VAL* 3.8 21.8 - - + -
37A PHE* 3.4 37.9 - + + -
51A HIS* 3.5 27.6 - + - -
52A LEU 3.0 6.4 + - - +
54A GLY* 1.3 72.2 - - - +
56A VAL* 1.3 65.5 + - - +
58A GLN* 3.5 2.2 + - - +
59A ALA* 3.2 22.5 + - - +
62A LEU* 4.0 18.2 - - + +
70A VAL* 4.0 15.6 - - + +
93A LYS 4.9 0.2 - - - +
94A VAL* 3.8 13.2 - - + +
129A SER* 4.5 7.0 - - - -
152A SER 3.7 16.8 - - - -
153A LEU 4.0 1.3 - - - -
154A ALA* 3.5 39.5 - - + -
157A ILE* 4.5 9.4 - - + -
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Residues in contact with VAL 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 3.0 28.3 + - + +
53A PRO* 3.6 10.8 - - + +
55A PHE* 1.3 76.6 - - - +
57A GLU* 1.3 64.1 + - + +
59A ALA* 3.2 17.8 + - - +
60A GLU* 4.4 1.6 - - - +
88A HIS 3.9 16.8 - - - +
89A LYS* 3.8 20.9 - - + +
90A ALA* 4.2 11.2 - - + -
93A LYS* 3.9 23.1 + - + +
94A VAL* 3.7 19.1 - - + -
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Residues in contact with GLU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A PRO* 2.8 33.6 + - + +
54A GLY* 3.7 11.1 - - - +
56A VAL* 1.3 74.4 - - + +
58A GLN* 1.3 72.6 + - - +
59A ALA 3.2 2.3 + - - -
60A GLU* 4.0 9.5 - - - +
61A ALA 5.6 0.3 + - - -
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Residues in contact with GLN 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A GLY* 3.0 20.3 + - - +
55A PHE 3.7 3.6 - - - +
56A VAL 3.2 0.2 - - - -
57A GLU* 1.3 88.9 + - + +
59A ALA* 1.3 64.8 + - - +
60A GLU 3.3 2.7 - - - -
61A ALA* 3.1 18.0 + - - +
62A LEU* 2.9 30.3 + - + +
154A ALA* 4.2 14.4 - - + -
155A PRO* 5.4 6.0 - - + +
158A ILE* 3.4 27.9 - - + +
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Residues in contact with ALA 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A PHE 3.2 10.2 + - - +
56A VAL 3.3 15.7 - - - +
57A GLU 3.2 3.2 - - - -
58A GLN* 1.3 76.7 - - - +
60A GLU* 1.3 64.6 + - + +
62A LEU* 3.4 7.8 + - - +
63A LYS* 3.1 38.2 + - - +
70A VAL* 5.8 1.7 - - - +
93A LYS* 3.6 39.7 - - + +
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Residues in contact with GLU 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A VAL 4.4 1.9 - - - +
57A GLU 4.0 9.7 - - - +
58A GLN 3.3 0.2 - - - -
59A ALA* 1.3 87.1 + - + +
61A ALA* 1.3 59.7 + - - +
62A LEU 3.1 0.2 - - - -
63A LYS* 3.3 12.7 + - + +
64A ALA* 2.9 29.3 + - - +
93A LYS* 3.7 24.3 + - - -
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Residues in contact with ALA 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A GLN* 3.1 31.1 + - - +
60A GLU* 1.3 75.6 - - - +
62A LEU* 1.3 62.6 + - - +
64A ALA* 3.2 19.0 + - - +
65A LYS* 3.5 19.5 + - - +
158A ILE* 4.2 10.1 - - + -
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Residues in contact with LEU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A VAL* 5.1 2.0 - - + -
55A PHE* 4.0 30.7 - - + +
58A GLN* 2.9 27.5 + - + +
59A ALA* 3.5 8.1 - - - +
61A ALA* 1.3 73.6 - - - +
63A LYS* 1.3 68.1 + - + +
64A ALA 3.0 1.3 - - - -
65A LYS* 2.9 13.4 + - - +
67A VAL* 3.0 35.4 + - + +
70A VAL* 4.0 18.4 - - + -
154A ALA* 5.4 0.7 - - + +
157A ILE* 4.0 15.3 - - + -
158A ILE* 3.7 27.6 - - + -
161A LEU* 3.9 14.8 - - + -
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Residues in contact with LYS 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ALA* 3.1 26.8 + - - +
60A GLU* 3.3 12.8 + - + +
62A LEU* 1.3 81.3 - - + +
64A ALA* 1.3 54.3 + - - +
66A GLY* 2.9 22.3 + - - -
67A VAL 3.4 18.2 - - - +
68A GLN* 3.7 22.2 + - - +
69A VAL* 5.3 1.6 - - - +
70A VAL* 5.7 5.4 - - + +
92A GLY 3.9 22.3 + - - -
93A LYS 5.1 6.2 + - - -
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Residues in contact with ALA 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A GLU 2.9 17.1 + - - +
61A ALA* 3.4 12.1 - - - +
62A LEU 3.0 0.6 - - - -
63A LYS* 1.3 75.0 - - - +
65A LYS* 1.3 59.8 + - + +
66A GLY 3.2 2.3 + - - -
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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) + - + + + + + -
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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