Contacts of the helix formed by residues 45 - 56 (chain C) in PDB entry 1H25
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 PRO 45 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15C TYR* 4.0 12.1 - - + -
35C ILE* 3.9 28.7 - - + -
36C ARG 4.2 7.6 - - - +
37C LEU* 4.3 5.2 - - + -
38C ASP* 5.8 3.4 - - - +
42C GLU 5.7 0.2 - - - +
43C GLY 3.7 6.5 - - - +
44C VAL* 1.3 96.0 - - + +
46C SER* 1.3 59.7 + - - +
47C THR* 4.0 14.8 - - - +
48C ALA* 3.0 24.7 + - + +
49C ILE* 3.3 7.1 + - - +
266D LYS* 5.4 0.4 - - - -
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Residues in contact with SER 46 (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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44C VAL 3.4 2.4 + - - -
45C PRO* 1.3 66.4 - - - +
47C THR* 1.3 73.0 + - - +
48C ALA 3.0 2.0 - - - -
49C ILE* 4.0 11.3 - - - +
50C ARG* 3.1 31.6 + - - +
266D LYS* 3.3 37.5 - - - +
272D PRO* 5.8 5.1 - - - +
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Residues in contact with THR 47 (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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14C THR* 4.9 6.5 + - - +
15C TYR* 3.8 20.1 - - - -
45C PRO* 4.0 7.4 - - - +
46C SER* 1.3 81.1 + - - +
48C ALA* 1.3 57.6 + - - +
50C ARG* 3.8 3.9 - - - +
51C GLU* 3.1 32.5 + - - +
147C GLY* 3.7 28.3 - - - +
148C LEU* 5.7 2.9 - - + -
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Residues in contact with ALA 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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15C TYR* 4.1 12.6 - - + -
35C ILE* 3.9 26.9 - - + -
44C VAL* 4.4 6.1 - - + -
45C PRO* 3.0 21.0 + - + +
47C THR* 1.3 78.0 + - - +
49C ILE* 1.3 67.5 + - - +
50C ARG 3.0 1.6 - - - -
51C GLU* 4.5 2.9 - - - -
52C ILE* 2.9 40.0 + - + +
76C LEU* 4.9 1.3 - - + -
78C LEU* 5.9 0.4 - - - -
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Residues in contact with ILE 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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44C VAL* 3.4 45.5 - - + +
45C PRO 3.3 8.4 + - - +
46C SER* 3.6 6.9 + - - +
48C ALA* 1.3 76.8 - - - +
50C ARG* 1.3 51.7 + - - +
53C SER* 2.7 41.7 + - - -
263D LEU* 3.9 18.2 - - + +
266D LYS* 3.9 19.7 - - + +
267D PHE* 4.5 15.7 - - + +
299D LEU* 4.4 12.8 - - + -
304D PHE* 4.4 10.2 - - + -
306D LEU* 3.7 31.0 - - + -
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Residues in contact with ARG 50 (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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46C SER* 3.1 23.1 + - - +
47C THR* 3.8 5.2 - - - +
48C ALA 3.0 0.6 - - - -
49C ILE* 1.3 75.1 - - - +
51C GLU* 1.3 59.2 + - - +
53C SER* 2.8 6.0 + - - -
54C LEU* 2.8 46.5 + - + +
126C ARG* 3.4 13.3 - - - +
146C PHE 5.1 1.1 - - - +
147C GLY 4.9 6.1 - - - +
148C LEU 5.6 0.4 - - - -
149C ALA 3.6 18.5 + - - +
150C ARG* 3.6 13.8 - - - +
160C TPO 2.8 44.2 + - - -
266D LYS 4.0 8.1 + - - +
267D PHE* 2.8 42.0 + - + +
268D GLU 3.6 13.9 + - - -
269D GLU 3.6 9.1 + - - -
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Residues in contact with GLU 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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15C TYR* 3.7 15.0 + - - -
33C LYS* 3.4 29.7 + - - +
47C THR* 3.1 14.1 + - - +
48C ALA* 3.8 3.6 - - - +
50C ARG* 1.3 77.1 - - - +
52C ILE* 1.3 54.2 + - + +
54C LEU* 5.1 0.4 - - - -
55C LEU* 2.8 53.8 + - + +
78C LEU* 4.4 13.7 - - + -
80C PHE* 3.5 12.0 - - - -
145C ASP* 4.8 1.1 - - - +
146C PHE* 3.5 28.5 + - - +
147C GLY* 3.2 24.6 - - - -
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Residues in contact with ILE 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 ALA* 2.9 27.1 + - + +
51C GLU* 1.3 72.3 - - - +
53C SER* 1.3 67.4 + - - +
55C LEU* 3.8 0.2 - - - +
56C LYS* 2.8 31.9 + - + +
66C LEU* 4.3 12.8 - - + -
69C VAL* 4.1 18.8 - - + -
76C LEU* 4.3 8.3 - - + -
78C LEU* 3.3 43.5 - - + -
304D PHE* 3.3 53.8 - - + -
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Residues in contact with SER 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 ILE* 2.7 28.7 + - - -
50C ARG 2.8 6.1 + - - -
52C ILE* 1.3 76.1 - - - +
54C LEU* 1.3 75.2 + - - +
56C LYS* 3.4 11.2 + - - +
57C GLU* 3.9 9.7 + - - +
267D PHE* 3.3 29.2 - - - -
304D PHE* 3.2 26.9 - - - +
305D ASP* 4.9 3.3 - - - +
306D LEU* 4.1 11.7 - - - -
307D ALA* 4.7 3.7 - - - +
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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 ARG* 2.8 24.9 + - + +
51C GLU* 4.2 1.6 - - - +
53C SER* 1.3 79.8 + - - +
55C LEU* 1.3 54.7 + - - +
56C LYS 2.4 18.8 + - - -
57C GLU* 2.5 27.2 + - + +
58C LEU* 4.0 13.5 + - + -
122C ARG* 5.3 1.8 - - - +
123C VAL* 4.2 20.9 - - + -
146C PHE* 5.3 3.6 - - + -
149C ALA* 4.3 9.0 - - + -
150C ARG* 3.9 37.0 - - - +
151C ALA* 3.9 22.2 - - + +
267D PHE* 4.1 5.8 - - + -
307D ALA* 4.0 19.7 - - + -
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Residues in contact with LEU 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 GLU* 2.8 36.6 + - + +
52C ILE 3.8 2.0 - - - +
54C LEU* 1.3 72.3 - - - +
56C LYS* 1.3 57.4 + - - +
57C GLU 2.9 15.5 - - - +
58C LEU* 3.4 15.6 - - + +
59C ASN* 5.4 1.0 + - - -
63C ILE* 4.2 7.2 - - + -
64C VAL* 4.2 18.8 - - + +
66C LEU* 4.2 22.9 + - + +
80C PHE* 3.4 35.2 - - + -
145C ASP 6.1 0.2 - - - +
146C PHE* 3.6 41.7 - - + +
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Residues in contact with LYS 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 ILE* 2.8 19.9 + - + +
53C SER 3.5 7.4 - - - +
54C LEU 2.4 13.1 + - - -
55C LEU* 1.3 65.4 - - - +
57C GLU* 1.3 67.2 + - - +
59C ASN* 5.3 3.8 + - - -
66C LEU* 4.3 17.9 - - + +
69C VAL* 5.6 4.0 - - + -
303D THR* 3.0 22.7 + - - +
304D PHE* 4.3 11.4 - - + -
305D ASP* 2.5 45.9 + - - +
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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