Contacts of the helix formed by residues 44 - 64 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41B GLY* 2.8 29.2 + - - +
42B ALA 3.1 8.0 - - - +
43B PHE* 1.3 79.5 - - - +
45B PRO* 1.3 71.4 - - + +
47B CYS* 3.0 19.8 - - - -
48B SER* 2.6 35.3 + - - -
120B PHE* 3.9 29.4 - - + -
124B ARG* 5.3 0.7 - - - +
1162B BEZ 3.3 11.9 + - + -
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Residues in contact with PRO 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B PHE 4.5 0.9 - - - +
44B THR* 1.3 86.9 - - - +
46B GLY* 1.3 56.6 + - - +
48B SER* 4.6 1.6 - - - -
49B LYS* 2.8 62.1 + - + +
1162B BEZ 3.2 20.0 - - + +
64C ALA 5.3 5.4 - - - +
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Residues in contact with GLY 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B PRO* 1.3 73.1 - - - +
47B CYS* 1.3 62.1 + - - +
49B LYS* 5.1 0.4 - - - -
50B THR* 3.0 24.3 + - - -
51B HIS* 3.0 8.8 + - - +
127B ARG* 4.5 0.4 - - - -
149B LEU* 3.9 27.5 - - - +
1162B BEZ 2.9 23.3 + - - -
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Residues in contact with CYS 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B VAL* 3.5 9.9 - - + -
40B PRO* 3.5 20.6 - - - -
41B GLY 3.5 14.4 - - - +
44B THR* 3.0 27.4 - - - +
45B PRO 3.3 0.2 - - - -
46B GLY* 1.3 75.6 - - - +
48B SER* 1.3 59.2 + - - +
51B HIS* 3.7 4.2 + - - -
52B LEU* 3.0 34.7 + - - +
84B TRP* 3.7 14.3 - - + -
127B ARG* 3.4 22.9 - - - +
1162B BEZ 3.1 14.3 + - - -
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Residues in contact with SER 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B PHE* 3.2 13.9 + - - -
44B THR 2.6 23.6 + - - -
45B PRO* 3.9 2.2 - - - -
47B CYS* 1.3 78.1 - - - +
49B LYS* 1.3 63.5 + - - +
50B THR 3.5 0.2 - - - -
53B PRO* 3.0 20.8 - - - +
84B TRP* 2.9 24.6 + - - -
88B HIS* 3.1 32.4 - - - -
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Residues in contact with LYS 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B PRO* 2.8 43.7 + - + +
46B GLY* 5.1 0.4 - - - -
48B SER* 1.3 77.0 - - - +
50B THR* 1.3 65.8 + - - +
53B PRO* 3.7 11.8 - - - +
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Residues in contact with THR 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B GLY* 3.0 12.2 + - - -
48B SER 3.5 0.2 - - - -
49B LYS* 1.3 86.4 + - - +
51B HIS* 1.3 67.2 + - - +
53B PRO* 3.6 3.5 - - - +
54B GLY* 3.1 21.3 + - - -
149B LEU* 3.9 22.8 - - + +
153B LEU* 4.1 27.1 - - + +
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Residues in contact with HIS 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B PHE* 3.6 22.8 - + - +
38B GLY 3.6 7.6 - - - -
39B VAL* 3.3 10.5 - - + +
46B GLY 3.0 8.0 + - - +
47B CYS* 3.9 7.6 - - - +
50B THR* 1.3 79.4 - - - +
52B LEU* 1.3 66.3 + - - +
54B GLY* 3.3 6.1 + - - -
55B PHE* 3.5 28.5 + + - -
127B ARG* 3.2 52.7 + - + +
128B PHE 3.9 5.4 - - - -
149B LEU* 4.4 0.9 - - + -
152B SER* 2.9 26.4 + - - -
153B LEU* 3.5 25.8 - - + -
154B ALA 5.5 0.5 + - - -
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Residues in contact with LEU 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B PHE* 4.0 16.3 - - + -
47B CYS 3.0 20.2 + - - +
48B SER* 5.2 0.2 - - - -
51B HIS* 1.3 73.8 - - - +
53B PRO* 1.3 65.2 - - + +
55B PHE* 3.0 13.0 + - - -
56B VAL* 3.1 23.8 + - + +
72B CYS* 4.6 3.4 - - + -
84B TRP* 3.7 47.3 - - + +
85B GLY* 4.8 4.0 - - - -
88B HIS* 4.0 21.8 - - + -
90B ALA* 4.9 0.9 - - + -
94B VAL* 3.9 28.3 - - + -
96B LEU* 4.6 11.4 - - + -
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Residues in contact with PRO 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B CYS 3.7 1.3 - - - +
48B SER 3.0 28.9 - - - +
49B LYS* 3.7 14.8 - - - +
50B THR 3.5 13.2 - - - +
52B LEU* 1.3 93.8 - - + +
54B GLY* 1.3 52.1 + - - +
56B VAL* 3.6 8.7 - - + +
57B GLU* 2.7 57.5 + - - +
88B HIS* 4.3 13.7 - - + +
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Residues in contact with GLY 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B THR 3.1 17.6 + - - -
51B HIS 3.3 2.2 + - - -
52B LEU 3.2 0.2 - - - -
53B PRO* 1.3 76.1 - - - +
55B PHE* 1.3 56.3 + - - +
57B GLU* 3.3 8.7 + - - +
58B GLN* 2.9 35.6 + - - +
154B ALA* 3.8 13.9 - - - -
155B PRO* 5.8 1.8 - - - -
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Residues in contact with PHE 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B VAL* 3.7 22.2 - - + -
37B PHE* 3.4 42.8 - + + -
51B HIS* 3.5 27.1 - + - -
52B LEU 3.0 7.5 + - - +
54B GLY* 1.3 73.1 - - - +
56B VAL* 1.3 65.4 + - - +
58B GLN* 3.9 2.2 - - - +
59B ALA* 3.4 17.5 + - - +
62B LEU* 3.9 20.9 - - + +
70B VAL* 4.1 7.5 - - + +
93B LYS 4.9 0.7 - - - +
94B VAL* 3.8 13.2 - - + +
129B SER* 4.5 5.2 - - - -
152B SER 3.7 17.0 - - - -
153B LEU 4.0 1.1 - - - -
154B ALA* 3.5 40.6 - - + -
157B ILE* 4.1 12.3 - - + -
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Residues in contact with VAL 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU* 3.1 27.4 + - + +
53B PRO* 3.6 9.6 - - + +
55B PHE* 1.3 76.3 - - - +
57B GLU* 1.3 67.4 + - + +
59B ALA* 3.2 19.8 + - - +
88B HIS 3.9 19.1 - - - +
89B LYS* 3.7 21.3 - - + +
90B ALA* 4.1 10.5 - - + -
93B LYS* 3.9 21.9 - - + +
94B VAL* 3.9 17.7 - - + -
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Residues in contact with GLU 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B PRO* 2.7 40.7 + - + +
54B GLY* 3.8 7.2 + - - +
56B VAL* 1.3 78.8 - - + +
58B GLN* 1.3 65.7 + - + +
59B ALA 3.3 2.5 + - - -
60B GLU* 4.9 2.1 + - - +
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Residues in contact with GLN 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B GLY* 2.9 20.1 + - - +
55B PHE 3.6 2.7 + - - -
56B VAL 3.2 0.2 - - - -
57B GLU* 1.3 83.5 + - + +
59B ALA* 1.3 65.2 + - - +
60B GLU 3.3 2.7 - - - -
61B ALA* 3.0 25.9 + - + +
62B LEU* 2.9 31.6 + - + +
154B ALA* 4.2 18.8 - - + -
155B PRO* 5.3 8.7 - - + +
158B ILE* 3.7 16.4 - - + +
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Residues in contact with ALA 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B PHE 3.4 7.9 + - - +
56B VAL 3.2 16.7 + - - +
57B GLU 3.3 1.4 + - - -
58B GLN* 1.3 77.0 - - - +
60B GLU* 1.3 61.4 + - + +
62B LEU* 3.3 7.9 + - - +
63B LYS* 3.0 38.5 + - + +
70B VAL* 6.1 1.3 - - - -
93B LYS* 3.7 39.3 - - + +
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Residues in contact with GLU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A SER* 2.5 40.2 + - - +
119A ILE* 3.7 17.5 - - + +
57B GLU 4.9 1.4 + - - -
58B GLN 3.3 0.6 - - - -
59B ALA* 1.3 79.8 - - + +
61B ALA* 1.3 61.1 + - - +
63B LYS* 3.2 26.6 + - - +
64B ALA* 2.8 30.0 + - - +
93B LYS* 6.5 0.9 - - - -
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Residues in contact with ALA 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B GLN* 3.0 37.7 + - - +
60B GLU* 1.3 78.1 - - - +
62B LEU* 1.3 62.6 + - - +
64B ALA* 3.3 15.3 + - - +
65B LYS* 3.4 19.9 + - - +
158B ILE* 4.1 11.6 - - + +
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Residues in contact with LEU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B VAL* 4.3 8.1 - - + -
55B PHE* 3.9 31.4 - - + +
58B GLN* 2.9 26.3 + - + +
59B ALA* 3.5 8.5 - - - +
61B ALA* 1.3 75.1 - - - +
63B LYS* 1.3 67.0 + - + +
65B LYS* 2.9 16.8 + - - +
67B VAL* 3.2 26.8 + - + +
70B VAL* 4.1 19.5 - - + -
154B ALA* 5.3 0.7 - - + +
157B ILE* 4.0 13.2 - - + -
158B ILE* 3.3 24.5 - - + -
161B LEU* 3.6 20.9 - - + -
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Residues in contact with LYS 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A SER* 2.8 34.4 + - - +
116A LEU* 4.0 22.6 - - + +
118A SER* 4.0 4.9 + - - -
119A ILE* 3.9 10.5 - - + -
1162A BEZ 4.0 3.1 - - - -
59B ALA* 3.0 24.7 + - + +
60B GLU* 3.3 29.4 + - - +
62B LEU* 1.3 75.8 - - + +
64B ALA* 1.3 56.5 + - - +
66B GLY* 2.8 20.6 + - - -
67B VAL 3.6 19.6 + - - +
68B GLN* 5.8 0.9 - - - -
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Residues in contact with ALA 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A PRO* 5.2 7.3 - - - +
116A LEU* 5.7 0.2 - - - -
119A ILE* 3.9 20.8 - - + +
1162A BEZ 3.5 20.5 + - - -
60B GLU 2.8 17.3 + - - +
61B ALA* 3.5 11.2 - - - +
62B LEU 3.1 0.4 - - - -
63B LYS* 1.3 74.9 - - - +
65B LYS* 1.3 60.2 + - + +
66B GLY 3.2 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