Contacts of the helix formed by residues 44 - 64 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41G GLY* 3.3 19.2 + - - +
42G ALA 3.2 4.4 - - - +
43G PHE* 1.3 78.4 - - - +
45G PRO* 1.3 69.2 - - - +
47G CYS* 3.0 28.2 - - - -
48G SER* 2.7 35.0 + - - -
120G PHE* 3.8 31.4 - - + -
124G ARG* 5.4 0.2 - - - +
1162G BEZ 3.0 14.3 + - - -
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Residues in contact with PRO 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43G PHE 4.4 2.0 - - - +
44G THR* 1.3 88.8 - - - +
46G GLY* 1.3 63.7 + - - +
48G SER* 3.3 2.9 + - - -
49G LYS* 2.9 36.0 + - + +
1162G BEZ 3.6 15.0 - - + +
64H ALA 5.2 6.5 - - - +
65H LYS* 6.3 3.4 - - + +
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Residues in contact with GLY 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G PRO* 1.3 73.7 - - - +
47G CYS* 1.3 63.3 + - - +
49G LYS* 5.4 0.2 - - - -
50G THR* 3.1 12.3 + - - -
51G HIS* 3.0 20.3 + - - +
127G ARG* 4.3 5.6 - - - -
149G LEU* 4.1 23.7 - - - +
1162G BEZ 2.7 27.3 + - - -
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Residues in contact with CYS 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G VAL* 3.6 13.2 - - + -
40G PRO* 3.5 18.2 - - - -
41G GLY 3.5 16.6 - - - +
44G THR* 3.0 25.6 - - - +
45G PRO 3.3 0.4 - - - -
46G GLY* 1.3 75.4 - - - +
48G SER* 1.3 58.7 + - - +
51G HIS* 4.0 3.1 - - - -
52G LEU* 2.9 35.5 + - - +
84G TRP* 3.8 10.3 - - + -
127G ARG* 3.3 28.5 - - - +
1162G BEZ 3.0 11.1 + - - -
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Residues in contact with SER 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43G PHE* 3.3 14.1 + - - -
44G THR 2.7 22.0 + - - -
45G PRO* 4.0 2.0 - - - -
47G CYS* 1.3 77.9 - - - +
49G LYS* 1.3 72.3 + - - +
50G THR 3.5 0.2 - - - -
53G PRO* 3.0 19.1 - - - +
84G TRP* 2.9 30.4 + - - +
88G HIS* 3.2 24.8 - - - -
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Residues in contact with LYS 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G PRO* 2.9 23.9 + - + +
46G GLY* 5.4 0.2 - - - -
48G SER* 1.3 87.8 - - - +
50G THR* 1.3 67.1 + - - +
53G PRO* 3.6 12.0 - - - +
88G HIS* 3.5 29.3 + - + -
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Residues in contact with THR 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G GLY* 3.1 9.9 + - - -
48G SER 3.5 0.4 - - - -
49G LYS* 1.3 85.0 + - - +
51G HIS* 1.3 67.5 + - - +
52G LEU 3.7 1.1 - - - -
53G PRO* 3.7 1.5 - - - +
54G GLY* 3.1 21.7 + - - -
149G LEU* 4.0 23.6 - - + +
153G LEU* 4.0 29.5 - - + +
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Residues in contact with HIS 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G PHE* 3.6 18.0 - + - +
38G GLY 3.5 12.8 - - - -
39G VAL* 3.5 10.0 - - + +
46G GLY 3.0 9.6 + - - +
47G CYS* 3.9 6.3 - - - +
50G THR* 1.3 79.2 - - - +
52G LEU* 1.3 65.4 + - - +
54G GLY* 3.4 5.4 + - - -
55G PHE* 3.5 29.8 + + - -
127G ARG* 3.0 55.7 + - + +
128G PHE 3.9 5.4 - - - -
149G LEU* 4.5 1.1 - - + -
152G SER* 2.9 26.8 + - - -
153G LEU* 3.6 22.9 - - + -
154G ALA 5.5 0.5 + - - -
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Residues in contact with LEU 52 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G PHE* 3.9 16.1 - - + -
39G VAL* 5.3 0.4 - - - +
47G CYS 2.9 18.1 + - - +
51G HIS* 1.3 73.2 - - - +
53G PRO* 1.3 69.2 - - + +
55G PHE* 3.0 5.5 + - - -
56G VAL* 3.0 30.7 + - + +
72G CYS* 4.5 1.3 - - + -
84G TRP* 3.7 42.4 - - + +
85G GLY* 4.9 2.9 - - - -
88G HIS* 3.9 24.9 - - + -
90G ALA* 5.0 0.7 - - + -
94G VAL* 3.9 28.7 - - + -
96G LEU* 4.3 15.9 - - + -
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Residues in contact with PRO 53 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47G CYS 3.7 1.6 - - - +
48G SER 3.0 26.9 - - - +
49G LYS* 3.6 19.3 - - - +
50G THR 3.6 6.7 - - - +
51G HIS 3.6 3.1 - - - -
52G LEU* 1.3 96.1 - - + +
54G GLY* 1.3 56.2 + - - +
56G VAL* 3.7 9.3 - - + +
57G GLU* 2.8 32.7 + - - +
88G HIS* 4.5 11.0 - - + +
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Residues in contact with GLY 54 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50G THR 3.1 19.3 + - - -
51G HIS 3.9 1.6 - - - -
52G LEU 3.1 0.4 + - - -
53G PRO* 1.3 75.5 - - - +
55G PHE* 1.3 57.1 + - - +
57G GLU* 3.8 3.7 - - - -
58G GLN* 2.9 37.4 + - - +
154G ALA* 3.7 13.5 - - - -
155G PRO* 6.0 1.3 - - - -
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Residues in contact with PHE 55 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35G VAL* 3.8 19.5 - - + -
37G PHE* 3.5 37.0 - + + -
51G HIS* 3.5 28.5 + + - -
52G LEU 3.0 7.1 + - - +
54G GLY* 1.3 72.1 - - - +
56G VAL* 1.3 66.0 + - - +
58G GLN* 3.8 2.1 - - - +
59G ALA* 3.4 18.4 + - - +
62G LEU* 3.8 27.2 - - + +
70G VAL* 4.1 9.0 - - + +
93G LYS 4.8 0.7 - - - +
94G VAL* 3.9 12.8 - - + +
129G SER* 4.5 2.5 - - - -
152G SER 3.7 18.2 - - - -
153G LEU 4.0 0.4 - - - -
154G ALA* 3.4 38.8 - - + -
157G ILE* 4.0 18.4 - - + -
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Residues in contact with VAL 56 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G LEU* 3.0 26.1 + - + +
53G PRO* 3.3 9.4 + - + +
55G PHE* 1.3 77.7 - - - +
57G GLU* 1.3 66.0 + - - +
59G ALA* 3.2 19.9 + - - +
60G GLU* 4.7 0.5 - - - +
88G HIS 4.0 17.5 - - - +
89G LYS* 3.8 13.7 - - + +
90G ALA* 4.0 16.4 - - + -
93G LYS* 3.6 30.8 - - + +
94G VAL* 3.9 17.7 - - + -
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Residues in contact with GLU 57 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G PRO 2.8 21.2 + - - +
54G GLY* 3.8 5.4 - - - +
56G VAL* 1.3 76.8 - - - +
58G GLN* 1.3 70.8 + - + +
59G ALA 3.2 3.5 + - - -
60G GLU* 3.9 9.9 - - - +
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Residues in contact with GLN 58 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54G GLY* 2.9 22.7 + - - +
55G PHE 3.7 4.9 + - - +
56G VAL 3.3 0.2 - - - -
57G GLU* 1.3 87.7 + - + +
59G ALA* 1.3 65.2 + - - +
60G GLU 3.3 2.7 - - - -
61G ALA* 3.1 24.1 + - + +
62G LEU* 2.9 31.2 + - + +
154G ALA* 4.0 21.5 - - + -
155G PRO* 5.3 9.3 - - + +
158G ILE* 4.6 11.3 - - + +
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Residues in contact with ALA 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55G PHE 3.4 8.1 + - - +
56G VAL 3.2 17.7 + - - +
57G GLU 3.2 1.8 - - - -
58G GLN* 1.3 77.2 - - - +
60G GLU* 1.3 65.6 + - - +
62G LEU* 3.3 7.7 + - - +
63G LYS* 3.0 39.8 + - - +
70G VAL* 6.0 1.6 - - - -
93G LYS* 3.9 34.1 - - + +
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Residues in contact with GLU 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118F SER* 4.8 14.8 + - - +
119F ILE* 4.0 25.0 - - + +
56G VAL 4.7 1.0 - - - +
57G GLU 3.9 12.3 - - - +
58G GLN 3.3 0.2 - - - -
59G ALA* 1.3 80.8 - - - +
61G ALA* 1.3 60.0 + - - +
63G LYS* 3.5 5.0 - - + +
64G ALA* 2.8 30.8 + - - +
93G LYS* 3.8 23.0 + - - -
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Residues in contact with ALA 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57G GLU 5.5 0.2 + - - -
58G GLN* 3.1 32.2 + - - +
60G GLU* 1.3 79.7 - - - +
62G LEU* 1.3 62.0 + - - +
64G ALA* 3.4 15.2 + - - +
65G LYS* 3.5 16.8 + - - +
158G ILE* 3.9 13.6 - - + +
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Residues in contact with LEU 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35G VAL* 4.6 2.2 - - + -
55G PHE* 3.8 32.3 - - + +
58G GLN* 2.9 28.0 + - + +
59G ALA* 3.7 4.9 - - - +
61G ALA* 1.3 74.8 - - - +
63G LYS* 1.3 65.8 + - - +
65G LYS* 2.9 12.9 + - - +
67G VAL* 3.1 35.6 + - + +
70G VAL* 3.8 21.5 - - + -
154G ALA 5.1 0.7 - - - +
157G ILE* 3.9 24.9 - - + -
158G ILE* 3.4 24.9 - - + -
161G LEU* 3.9 9.2 - - + -
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Residues in contact with LYS 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115F SER* 2.7 31.1 + - - +
116F LEU* 3.7 14.5 - - + +
118F SER* 3.2 26.9 - - - +
119F ILE* 3.6 22.2 - - + +
1162F BEZ 3.6 2.9 - - - -
59G ALA* 3.0 23.9 + - - +
60G GLU* 3.2 10.5 + - - +
62G LEU* 1.3 75.6 - - + +
64G ALA* 1.3 55.2 + - - +
66G GLY* 2.7 24.4 + - - -
67G VAL 3.4 20.7 + - - +
68G GLN 4.5 8.9 + - - -
92G GLY 4.8 14.1 + - - -
93G LYS* 6.1 0.2 - - - +
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Residues in contact with ALA 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F PRO* 5.2 5.7 - - - +
119F ILE* 3.7 14.8 - - + +
1162F BEZ 3.1 23.1 + - - -
60G GLU 2.8 16.8 + - - +
61G ALA* 3.5 11.0 - - - +
62G LEU 3.1 0.4 - - - -
63G LYS* 1.3 76.4 - - - +
65G LYS* 1.3 63.1 + - + +
66G GLY 3.3 0.7 - - - -
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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) + - + + + + + -
------------------------------------------------------------
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