Contacts of the helix formed by residues 44 - 59 (chain C) in PDB entry 1H88
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41C THR* 6.4 0.2 - - + -
42C ARG* 4.2 8.1 - - - +
43C TRP* 1.3 73.7 - - - +
45C ARG* 1.3 65.5 + - - +
46C GLU* 3.4 9.6 + - - +
47C GLU* 3.1 34.6 + - - +
48C ASP* 3.1 26.5 + - - +
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Residues in contact with ARG 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C TRP 4.6 4.0 + - - -
44C THR* 1.3 72.6 + - - +
46C GLU* 1.3 64.9 + - - +
48C ASP* 3.0 38.9 + - - +
49C GLU* 3.0 23.4 + - - +
81C ARG* 3.9 9.1 - - - +
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Residues in contact with GLU 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C THR* 3.2 9.5 + - - +
45C ARG* 1.3 75.3 - - - +
47C GLU* 1.3 57.0 + - + +
49C GLU* 2.7 13.7 + - - +
50C LYS* 2.6 56.5 + - + +
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Residues in contact with GLU 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C THR* 5.3 0.9 - - - +
42C ARG 4.0 1.2 - - - +
43C TRP* 3.5 17.0 - - + -
44C THR* 3.1 36.7 + - - +
46C GLU* 1.3 80.5 - - + +
48C ASP* 1.3 65.9 + - - +
50C LYS* 3.6 2.1 - - - +
51C LEU* 2.7 26.0 + - - +
70C LEU* 4.0 25.4 - - + +
71C PRO 4.1 6.8 - - - +
72C ASN* 4.9 6.4 + - - +
73C ARG* 3.2 42.2 + - - +
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Residues in contact with ASP 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C TRP* 3.4 9.4 - - - +
44C THR 3.1 21.0 + - - +
45C ARG* 3.0 32.1 + - - +
47C GLU* 1.3 77.9 - - - +
49C GLU* 1.3 62.7 + - - +
51C LEU* 3.3 0.4 + - - -
52C LYS* 2.9 32.8 + - + +
81C ARG* 3.0 32.7 + - - -
85C VAL* 5.1 0.3 - - - +
86C LEU* 3.1 37.6 - - + +
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Residues in contact with GLU 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C ARG 3.0 14.2 + - - +
46C GLU* 2.7 16.4 + - - +
48C ASP* 1.3 72.1 - - - +
50C LYS* 1.3 58.0 + - - +
52C LYS* 2.8 45.3 + - - +
53C LYS* 2.9 35.3 + - + +
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Residues in contact with LYS 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C GLU* 2.6 40.1 + - + +
47C GLU* 3.6 4.7 - - - +
49C GLU* 1.3 72.9 - - - +
51C LEU* 1.3 56.7 + - - +
53C LYS* 3.7 20.5 + - - +
54C LEU* 3.0 40.9 + - + +
69C TYR* 3.4 37.2 + - - +
70C LEU* 3.9 20.4 - - + -
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Residues in contact with LEU 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C TRP* 4.4 2.5 - - + -
47C GLU 2.7 19.9 + - - +
48C ASP 3.7 2.5 - - - +
50C LYS* 1.3 71.1 - - - +
52C LYS* 1.3 61.5 + - - +
54C LEU* 3.5 3.9 - - - +
55C VAL* 2.8 44.0 + - + +
63C TRP* 4.5 0.7 - - + -
66C ILE* 3.3 31.6 - - + -
70C LEU* 3.6 21.7 - - + +
78C CYS* 3.6 31.4 - - + +
81C ARG* 4.3 7.9 - - + -
82C TRP* 3.7 17.5 - - + +
86C LEU* 3.6 24.2 - - + -
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Residues in contact with LYS 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C ASP* 2.9 30.1 + - + +
49C GLU* 2.8 27.3 + - - +
51C LEU* 1.3 77.4 - - - +
53C LYS* 1.3 62.7 + - + +
55C VAL* 3.5 3.7 + - - +
56C GLU* 2.8 42.0 + - - +
82C TRP* 4.9 5.2 - - + +
86C LEU* 3.6 39.8 - - + +
88C PRO* 6.0 4.3 - - + -
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Residues in contact with LYS 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C GLU* 2.9 33.3 + - + +
50C LYS* 3.7 29.0 - - - +
52C LYS* 1.3 77.8 - - + +
54C LEU* 1.3 62.0 + - - +
56C GLU* 3.2 17.9 + - - +
57C GLN* 3.3 25.4 + - - +
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Residues in contact with LEU 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C LYS* 3.0 31.8 + - + +
51C LEU* 3.5 5.8 - - - +
53C LYS* 1.3 76.8 - - + +
55C VAL* 1.3 63.0 + - - +
57C GLN* 3.3 11.8 + - - +
58C ASN* 3.0 35.4 + - - +
66C ILE* 3.4 38.6 - - + +
69C TYR* 3.3 60.3 - - + -
70C LEU* 4.6 4.0 - - + -
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Residues in contact with VAL 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C LEU* 2.8 29.5 + - + +
52C LYS 3.8 3.6 - - - +
54C LEU* 1.3 69.3 - - - +
56C GLU* 1.3 74.0 + - - +
59C GLY* 2.7 41.0 + - - +
60C THR* 4.7 1.3 - - - +
63C TRP* 3.9 15.5 - - + -
66C ILE* 3.8 20.6 - - + -
82C TRP* 3.6 50.0 - - + +
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Residues in contact with GLU 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C LYS* 2.8 27.9 + - - +
53C LYS* 3.3 13.4 - - - +
55C VAL* 1.3 85.5 - - - +
57C GLN* 1.3 64.4 + - + +
59C GLY* 4.5 1.6 + - - -
82C TRP* 4.6 7.5 + - - -
88C PRO* 5.4 10.4 - - - +
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Residues in contact with GLN 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C LYS* 3.3 21.1 + - - +
54C LEU* 3.8 11.9 + - - +
55C VAL 3.2 0.4 - - - -
56C GLU* 1.3 81.8 - - + +
58C ASN* 1.3 76.3 + - - +
59C GLY 3.6 0.3 + - - -
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Residues in contact with ASN 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C LEU* 3.0 23.3 + - - +
57C GLN* 1.3 89.0 + - - +
59C GLY* 1.3 59.2 + - - +
61C ASP* 5.1 1.4 + - - +
62C ASP* 3.5 39.6 + - + +
65C VAL* 3.9 18.8 - - - +
66C ILE* 4.6 11.6 - - + +
69C TYR* 5.5 1.5 - - - -
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Residues in contact with GLY 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C VAL* 2.7 40.5 + - - +
56C GLU 5.1 1.3 - - - -
57C GLN 3.5 1.8 - - - -
58C ASN* 1.3 74.5 - - - +
60C THR* 1.3 60.7 + - - -
61C ASP* 3.3 6.4 + - - -
62C ASP 4.5 2.0 + - - -
63C TRP* 4.6 0.7 - - - -
66C ILE* 4.1 10.4 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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