Contacts of the helix formed by residues 44 - 64 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41H GLY* 2.9 27.7 + - - +
42H ALA 3.1 7.6 - - - +
43H PHE* 1.3 79.3 - - - +
45H PRO* 1.3 70.4 - - - +
47H CYS* 3.1 19.6 - - - -
48H SER* 2.7 35.7 + - - -
120H PHE* 3.9 30.3 - - + -
124H ARG* 5.2 0.2 - - - +
1162H BEZ 3.3 13.3 + - + -
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Residues in contact with PRO 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43H PHE 4.4 1.8 - - - +
44H THR* 1.3 85.1 - - + +
46H GLY* 1.3 57.9 + - - +
48H SER* 4.6 1.8 - - - -
49H LYS* 2.8 65.6 + - + +
1162H BEZ 3.3 18.8 - - + +
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Residues in contact with GLY 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45H PRO* 1.3 74.7 - - - +
47H CYS* 1.3 59.0 + - - +
49H LYS* 5.2 0.4 - - - -
50H THR* 3.0 14.1 + - - -
51H HIS* 3.0 22.9 + - - +
127H ARG* 4.4 0.4 - - - -
149H LEU* 3.9 26.5 - - - +
1162H BEZ 2.8 23.7 + - - -
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Residues in contact with CYS 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39H VAL* 3.5 18.6 - - + -
40H PRO* 3.6 11.9 - - - -
41H GLY 3.5 16.6 - - - +
44H THR* 3.1 23.8 - - - +
45H PRO 3.3 0.2 - - - -
46H GLY* 1.3 77.8 - - - +
48H SER* 1.3 59.0 + - - +
51H HIS* 3.6 3.8 + - - -
52H LEU* 3.0 33.8 + - - +
84H TRP* 3.6 15.3 - - + -
127H ARG* 3.3 25.6 - - - +
1162H BEZ 3.1 11.7 + - - -
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Residues in contact with SER 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43H PHE* 3.3 13.7 + - - -
44H THR 2.7 25.0 + - - -
45H PRO* 4.0 2.9 - - - -
47H CYS* 1.3 78.5 - - - +
49H LYS* 1.3 62.7 + - - +
53H PRO* 3.1 20.5 - - - +
84H TRP* 2.9 28.7 + - - +
88H HIS* 3.1 26.4 - - - -
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Residues in contact with LYS 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45H PRO* 2.8 45.6 + - + +
46H GLY* 5.2 0.2 - - - -
48H SER* 1.3 79.1 - - - +
50H THR* 1.3 66.5 + - - +
53H PRO* 3.8 12.1 - - - +
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Residues in contact with THR 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46H GLY* 3.0 11.2 + - - -
48H SER 3.5 0.2 - - - -
49H LYS* 1.3 87.1 + - - +
51H HIS* 1.3 68.6 + - - +
52H LEU 3.6 0.9 - - - -
53H PRO* 3.7 1.9 - - - +
54H GLY* 3.1 21.0 + - - -
149H LEU* 4.1 24.6 - - + +
153H LEU* 4.1 26.5 - - + +
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Residues in contact with HIS 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H PHE* 3.6 17.5 - + - +
38H GLY 3.5 12.8 - - - -
39H VAL* 3.4 11.7 - - + +
46H GLY 3.0 8.8 + - - +
47H CYS* 3.6 7.4 + - - +
50H THR* 1.3 79.8 - - - +
52H LEU* 1.3 65.5 + - - +
54H GLY* 3.3 5.2 + - - -
55H PHE* 3.4 29.0 + + - -
127H ARG* 3.1 56.4 + - + +
128H PHE 4.0 4.9 - - - -
149H LEU* 4.4 3.1 - - + -
152H SER* 3.0 27.6 + - - -
153H LEU* 3.7 18.2 - - + -
154H ALA 5.5 0.7 + - - -
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Residues in contact with LEU 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H PHE* 4.0 15.7 - - + -
47H CYS 3.0 17.6 + - - +
51H HIS* 1.3 72.5 - - - +
53H PRO* 1.3 70.0 - - + +
55H PHE* 3.0 4.9 + - - +
56H VAL* 3.0 28.3 + - + +
72H CYS* 4.7 4.0 - - + -
84H TRP* 3.8 45.5 - - + +
85H GLY* 4.7 3.1 - - - -
88H HIS* 3.8 27.8 - - + -
90H ALA* 4.9 0.9 - - + -
94H VAL* 4.0 27.6 - - + -
96H LEU* 4.5 11.0 - - + -
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Residues in contact with PRO 53 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47H CYS 3.7 2.9 - - - +
48H SER 3.1 28.3 - - - +
49H LYS 3.8 14.1 - - - +
50H THR* 3.7 7.9 - - - +
51H HIS 3.6 2.2 - - - -
52H LEU* 1.3 95.6 - - + +
54H GLY* 1.3 55.6 + - - +
56H VAL* 3.7 9.3 - - + +
57H GLU* 2.8 50.2 + - - +
88H HIS* 4.3 13.7 - - + +
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Residues in contact with GLY 54 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50H THR 3.1 19.3 + - - -
51H HIS 3.3 1.5 + - - -
52H LEU 3.1 0.4 - - - -
53H PRO* 1.3 78.1 - - - +
55H PHE* 1.3 56.4 + - - +
57H GLU* 3.9 11.0 + - - +
58H GLN* 3.0 36.9 + - - +
154H ALA* 3.7 13.2 - - - -
155H PRO* 5.9 1.6 - - - -
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Residues in contact with PHE 55 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H VAL* 3.8 18.4 - - + -
37H PHE* 3.3 53.2 - + + -
51H HIS* 3.4 32.8 - + - -
52H LEU 3.0 6.1 + - - +
54H GLY* 1.3 74.1 - - - +
56H VAL* 1.3 66.5 + - - +
58H GLN* 3.7 3.1 + - - +
59H ALA* 3.4 17.5 + - - +
62H LEU* 4.0 21.1 - - + +
70H VAL* 4.2 5.6 - - + -
93H LYS 4.9 0.5 - - - +
94H VAL* 3.8 14.1 - - + +
129H SER* 4.5 0.2 - - - -
152H SER 3.7 7.6 - - - -
153H LEU 4.1 0.7 - - - -
154H ALA* 3.6 38.8 - - + -
157H ILE* 4.2 19.1 - - + -
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Residues in contact with VAL 56 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52H LEU* 3.0 30.4 + - + +
53H PRO* 3.2 10.3 + - + +
55H PHE* 1.3 77.3 - - - +
57H GLU* 1.3 65.5 + - + +
59H ALA* 3.2 19.8 + - - +
88H HIS 3.9 18.2 - - - +
89H LYS* 3.7 20.4 - - + +
90H ALA* 4.1 12.1 - - + -
93H LYS* 3.9 22.8 + - + +
94H VAL* 3.8 19.1 - - + -
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Residues in contact with GLU 57 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53H PRO* 2.8 35.8 + - + +
54H GLY* 3.9 12.3 + - - +
56H VAL* 1.3 76.8 - - + +
58H GLN* 1.3 69.2 + - - +
59H ALA 3.3 2.9 + - - -
60H GLU* 4.9 2.1 + - - +
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Residues in contact with GLN 58 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54H GLY* 3.0 19.9 + - - +
55H PHE 3.8 3.6 - - - +
56H VAL 3.3 0.4 - - - -
57H GLU* 1.3 86.8 + - - +
59H ALA* 1.3 64.2 + - - +
60H GLU 3.3 2.9 - - - -
61H ALA* 3.1 24.3 + - + +
62H LEU* 2.9 31.0 + - + +
154H ALA* 4.0 20.4 - - + -
155H PRO* 5.3 7.9 - - + +
158H ILE* 4.7 9.0 - - + +
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Residues in contact with ALA 59 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55H PHE 3.4 7.9 + - - +
56H VAL 3.2 17.9 + - - +
57H GLU 3.3 1.6 - - - -
58H GLN* 1.3 76.6 - - - +
60H GLU* 1.3 61.9 + - + +
62H LEU* 3.3 8.6 + - - +
63H LYS* 3.0 37.3 + - + +
70H VAL* 5.9 1.6 - - - -
93H LYS* 3.9 37.5 - - + +
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Residues in contact with GLU 60 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118G SER* 2.3 32.1 + - - -
119G ILE* 3.2 24.8 - - + +
57H GLU 4.9 2.2 + - - +
58H GLN 3.3 0.4 - - - -
59H ALA* 1.3 79.3 - - + +
61H ALA* 1.3 61.9 + - - +
63H LYS* 3.0 35.0 + - - +
64H ALA* 2.8 30.0 + - - +
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Residues in contact with ALA 61 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57H GLU 5.7 0.2 + - - -
58H GLN* 3.1 33.0 + - - +
60H GLU* 1.3 76.9 - - - +
62H LEU* 1.3 62.7 + - - +
64H ALA* 3.3 15.5 + - - +
65H LYS* 3.4 19.4 + - - +
158H ILE* 4.1 14.0 - - + +
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Residues in contact with LEU 62 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H VAL* 4.5 6.7 - - + -
55H PHE* 4.0 31.9 - - + +
58H GLN* 2.9 27.7 + - + +
59H ALA* 3.6 7.2 - - - +
61H ALA* 1.3 73.3 - - - +
63H LYS* 1.3 66.9 + - + +
65H LYS* 2.9 15.2 + - - +
67H VAL* 3.2 29.6 + - + +
70H VAL* 4.2 20.2 - - + -
154H ALA* 5.3 0.9 - - + +
157H ILE* 3.9 13.5 - - + -
158H ILE* 3.3 25.6 - - + -
161H LEU* 3.6 20.0 - - + -
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Residues in contact with LYS 63 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115G SER* 2.9 33.8 + - - +
116G LEU* 4.1 20.0 - - + +
118G SER* 4.1 3.4 + - - -
119G ILE* 4.0 9.9 - - + -
1162G BEZ 4.1 5.7 - - - -
59H ALA* 3.0 23.2 + - + +
60H GLU* 3.0 33.6 + - - +
62H LEU* 1.3 76.8 - - + +
64H ALA* 1.3 58.0 + - - +
65H LYS 3.1 0.2 - - - -
66H GLY* 2.9 21.0 + - - -
67H VAL 3.6 19.6 - - - +
68H GLN* 5.7 0.9 - - - -
70H VAL* 6.5 0.7 - - + -
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Residues in contact with ALA 64 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G PRO* 5.2 8.0 - - - +
119G ILE* 3.9 21.0 - - + +
1162G BEZ 3.5 23.2 + - - -
60H GLU 2.8 17.0 + - - +
61H ALA* 3.5 10.3 - - - +
62H LEU 3.1 0.6 - - - -
63H LYS* 1.3 75.8 - - - +
65H LYS* 1.3 58.8 + - + +
66H GLY 3.2 1.3 - - - -
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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) + - + + + + + -
------------------------------------------------------------
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