Contacts of the helix formed by residues 44 - 64 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41D GLY* 2.9 28.0 + - - +
42D ALA 3.7 8.1 - - - +
43D PHE* 1.3 78.8 - - - +
45D PRO* 1.3 70.3 - - - +
47D CYS* 3.1 19.1 - - - -
48D SER* 2.6 34.9 + - - -
120D PHE* 3.8 28.3 - - + -
124D ARG* 5.2 0.9 - - - +
1162D BEZ 3.1 12.4 + - - -
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Residues in contact with PRO 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D PHE 4.6 1.1 - - - +
44D THR* 1.3 86.0 - - - +
46D GLY* 1.3 56.6 + - - +
48D SER* 4.6 1.6 - - - -
49D LYS* 2.9 61.7 + - + +
1162D BEZ 3.3 20.0 - - + +
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Residues in contact with GLY 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D PRO* 1.3 72.0 - - - +
47D CYS* 1.3 62.1 + - - +
49D LYS* 5.2 1.8 - - - -
50D THR* 3.1 13.1 + - - -
51D HIS* 3.0 20.3 + - - +
127D ARG* 4.2 7.0 - - - -
149D LEU* 4.0 21.9 - - - +
1162D BEZ 2.7 24.8 + - - -
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Residues in contact with CYS 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D VAL* 3.5 7.6 - - + -
40D PRO* 3.5 21.3 - - - -
41D GLY 3.5 17.0 - - - +
44D THR* 3.1 25.8 - - - +
45D PRO 3.3 0.2 - - - -
46D GLY* 1.3 76.9 - - - +
48D SER* 1.3 58.8 + - - +
51D HIS* 4.0 2.9 - - - -
52D LEU* 3.0 34.7 + - - +
84D TRP* 3.7 15.0 - - + -
127D ARG* 3.2 25.4 - - - +
1162D BEZ 3.0 11.8 + - - -
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Residues in contact with SER 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D PHE* 3.2 13.9 + - - -
44D THR 2.6 26.8 + - - -
45D PRO* 4.0 2.2 - - - -
47D CYS* 1.3 77.7 - - - +
49D LYS* 1.3 62.3 + - - +
53D PRO* 3.0 20.0 - - - +
84D TRP* 2.9 25.0 + - - -
88D HIS* 3.1 32.3 - - - -
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Residues in contact with LYS 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D PRO* 2.9 43.7 + - + +
46D GLY* 5.2 1.3 - - - -
48D SER* 1.3 79.9 - - - +
50D THR* 1.3 66.6 + - - +
53D PRO* 3.6 11.5 - - - +
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Residues in contact with THR 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D GLY* 3.1 11.4 + - - -
48D SER 3.5 0.2 - - - -
49D LYS* 1.3 86.6 + - - +
51D HIS* 1.3 69.4 + - - +
53D PRO* 3.6 3.3 - - - +
54D GLY* 3.1 21.0 + - - -
149D LEU* 3.9 25.0 - - + +
153D LEU* 4.0 27.6 - - + +
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Residues in contact with HIS 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D PHE* 3.6 18.4 - + - +
38D GLY 3.5 12.1 - - - -
39D VAL* 3.5 9.1 - - + +
46D GLY 3.0 6.2 + - - +
47D CYS* 3.9 6.3 - - - +
50D THR* 1.3 81.5 - - - +
52D LEU* 1.3 65.9 + - - +
54D GLY* 3.3 5.5 + - - -
55D PHE* 3.4 24.2 + + - -
127D ARG* 3.1 57.8 + - + +
128D PHE 3.9 5.2 - - - -
149D LEU* 4.3 1.3 - - + -
152D SER* 2.9 25.4 + - - -
153D LEU* 3.6 22.7 - - + -
154D ALA 5.5 0.5 + - - -
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Residues in contact with LEU 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D PHE* 4.0 15.4 - - + -
39D VAL* 5.3 0.2 - - - +
47D CYS 3.0 18.1 + - - +
51D HIS* 1.3 73.1 - - - +
53D PRO* 1.3 68.2 - - + +
55D PHE* 3.0 4.9 + - - +
56D VAL* 3.0 30.8 + - + +
72D CYS* 4.5 4.7 - - + -
84D TRP* 3.8 43.3 - - + +
85D GLY* 4.8 2.9 - - - -
88D HIS* 3.9 25.1 - - + -
90D ALA* 4.9 0.7 - - + -
94D VAL* 3.8 29.2 - - + -
96D LEU* 4.5 12.1 - - + -
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Residues in contact with PRO 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D CYS 3.6 3.1 - - - +
48D SER 3.0 28.9 - - - +
49D LYS 3.6 17.7 - - - +
50D THR 3.6 6.3 - - - +
51D HIS 3.6 2.2 - - - -
52D LEU* 1.3 95.6 - - + +
54D GLY* 1.3 55.9 + - - +
56D VAL* 3.7 9.6 - - + +
57D GLU* 2.8 36.2 + - - +
88D HIS* 4.4 11.7 - - + +
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Residues in contact with GLY 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D THR 3.1 18.9 + - - -
51D HIS 3.9 1.6 - - - -
52D LEU 3.2 0.2 - - - -
53D PRO* 1.3 75.7 - - - +
55D PHE* 1.3 57.1 + - - +
57D GLU* 2.9 19.1 - - - +
58D GLN* 2.9 33.1 + - - +
154D ALA* 3.8 12.6 - - - -
155D PRO* 5.9 2.2 - - - -
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Residues in contact with PHE 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D VAL* 3.9 22.7 - - + -
37D PHE* 3.4 39.0 - + + -
51D HIS* 3.4 39.4 + + - -
52D LEU 3.0 7.4 + - - +
54D GLY* 1.3 73.8 - - - +
56D VAL* 1.3 66.9 + - - +
58D GLN* 3.9 1.8 - - - +
59D ALA* 3.4 17.7 + - - +
62D LEU* 3.7 24.2 - - + +
70D VAL* 4.0 9.9 - - + +
93D LYS 4.8 0.3 - - - +
94D VAL* 3.7 13.0 - - + +
129D SER* 4.4 0.7 - - - -
152D SER 3.7 7.6 - - - -
153D LEU 4.1 1.3 - - - -
154D ALA* 3.6 38.8 - - + -
157D ILE* 4.4 13.5 - - + -
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Residues in contact with VAL 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D LEU* 3.0 29.0 + - + +
53D PRO* 3.7 9.9 - - + +
55D PHE* 1.3 77.8 - - - +
57D GLU* 1.3 62.7 - - - +
59D ALA* 3.2 19.2 + - - +
60D GLU* 4.7 0.7 - - - +
88D HIS 3.9 18.2 - - - +
89D LYS* 3.8 20.6 - - + +
90D ALA* 4.0 13.2 - - + -
93D LYS* 3.5 22.4 - - + +
94D VAL* 3.8 18.4 - - + -
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Residues in contact with GLU 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D PRO* 2.8 18.8 + - - +
54D GLY* 2.9 31.6 - - - +
56D VAL* 1.3 76.1 - - - +
58D GLN* 1.3 83.4 + - - +
59D ALA 3.3 3.2 + - - -
60D GLU* 3.6 11.4 - - - +
61D ALA 5.6 0.2 + - - -
155D PRO* 5.7 3.1 - - - +
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Residues in contact with GLN 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D GLY 2.9 20.5 + - - +
55D PHE 3.9 2.0 - - - -
57D GLU* 1.3 108.3 + - + +
59D ALA* 1.3 63.5 + - - +
60D GLU 3.3 2.9 - - - -
61D ALA* 3.1 15.8 + - - +
62D LEU* 2.9 26.7 + - + +
154D ALA* 3.9 15.5 - - + -
155D PRO* 5.1 8.2 - - + +
158D ILE* 3.5 30.1 - - + +
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Residues in contact with ALA 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D PHE 3.4 8.3 + - - +
56D VAL 3.2 17.4 + - - +
57D GLU 3.3 1.6 - - - -
58D GLN* 1.3 76.4 - - - +
60D GLU* 1.3 66.0 + - - +
62D LEU* 3.3 8.9 + - - +
63D LYS* 2.9 43.7 + - - +
70D VAL* 6.0 2.2 - - - -
93D LYS* 4.0 33.2 - - + +
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Residues in contact with GLU 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C SER* 4.6 16.8 + - - +
119C ILE* 3.8 26.5 - - + +
56D VAL 4.7 0.3 - - - +
57D GLU 3.6 16.3 - - - +
59D ALA* 1.3 78.9 - - - +
61D ALA* 1.3 59.1 + - - +
63D LYS* 3.2 4.5 + - - +
64D ALA* 2.9 29.6 + - - +
93D LYS* 2.9 28.2 + - - -
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Residues in contact with ALA 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D GLN* 3.1 31.5 + - - +
60D GLU* 1.3 80.5 - - - +
62D LEU* 1.3 60.5 + - - +
64D ALA* 3.4 18.7 + - - +
65D LYS* 3.5 14.4 + - - +
158D ILE* 4.0 16.6 - - + +
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Residues in contact with LEU 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D VAL* 4.7 2.9 - - + -
55D PHE* 3.7 34.8 - - + +
58D GLN* 2.9 28.7 + - + +
59D ALA* 3.6 5.2 - - - +
61D ALA* 1.3 75.4 - - - +
63D LYS* 1.3 64.0 + - + +
65D LYS* 3.0 11.8 + - - +
67D VAL* 3.1 36.7 + - + +
70D VAL* 4.1 17.7 - - + -
154D ALA 4.9 0.2 - - - +
157D ILE* 3.9 13.9 - - + -
158D ILE* 3.6 26.5 - - + -
161D LEU* 3.8 20.0 - - + -
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Residues in contact with LYS 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C SER* 2.9 37.4 + - - +
116C LEU* 3.7 15.9 - - + +
118C SER* 3.4 26.2 - - - +
119C ILE* 3.7 17.1 - - + +
1162C BEZ 3.6 6.8 - - - -
59D ALA* 2.9 32.5 + - - +
60D GLU* 3.2 5.8 + - - +
62D LEU* 1.3 75.3 - - + +
64D ALA* 1.3 53.9 + - - +
66D GLY* 2.7 24.8 + - - -
67D VAL 3.5 17.8 + - - +
68D GLN 4.4 5.5 + - - -
69D VAL* 5.9 0.4 - - - +
70D VAL* 6.5 0.7 - - + -
92D GLY 4.5 17.5 + - - -
93D LYS* 5.7 3.2 + - - +
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Residues in contact with ALA 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C PRO* 5.1 6.4 - - - +
119C ILE* 3.7 15.2 - - + +
1162C BEZ 3.1 22.5 + - - -
60D GLU 2.9 16.4 + - - +
61D ALA* 3.5 11.0 - - - +
62D LEU 3.1 0.4 - - - -
63D LYS* 1.3 75.7 - - - +
65D LYS* 1.3 61.4 + - + +
66D GLY 3.3 1.1 - - - -
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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