Contacts of the helix formed by residues 51 - 59 (chain C) in PDB entry 1C3Q
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 GLU 51 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68B THR* 5.5 0.2 - - - -
69B LEU* 3.5 18.8 + - - +
101B THR* 2.9 29.8 + - - +
103B PHE* 4.2 10.1 - - + -
104B ARG* 2.7 47.6 + - - +
46C ALA* 3.6 19.7 - - + +
47C TYR 4.8 0.5 + - - -
48C ALA* 2.9 17.9 + - + +
50C GLU* 1.3 81.4 - - - +
52C VAL* 1.3 66.7 + - - +
53C ALA* 3.3 2.9 - - - -
54C ASP* 3.3 11.7 + - - +
55C MET* 3.1 22.2 + - - +
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Residues in contact with VAL 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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21C HIS* 3.9 7.9 - - + -
23C ILE* 4.1 11.4 - - + -
46C ALA 3.5 27.4 - - - +
47C TYR* 3.5 14.1 - - - +
48C ALA 2.9 26.8 + - - +
49C LYS* 3.8 15.0 + - - +
51C GLU* 1.3 70.0 - - - +
53C ALA* 1.3 67.5 + - - +
55C MET* 4.5 1.3 - - - -
56C ALA* 3.0 27.2 + - - +
76C ALA* 3.8 19.5 - - + +
79C ILE* 4.0 14.1 - - + -
80C ALA* 3.9 11.9 - - + +
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Residues in contact with ALA 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 LYS 5.0 2.6 + - - +
51C GLU 3.3 1.2 - - - -
52C VAL* 1.3 82.7 - - - +
54C ASP* 1.3 68.3 + - - +
57C LYS* 3.2 14.6 + - - +
79C ILE* 4.2 17.9 - - + -
80C ALA* 4.8 0.2 - - - +
83C SER* 2.8 39.0 + - - +
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Residues in contact with ASP 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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101B THR* 4.7 13.6 - - + -
102B PRO* 4.1 24.0 - - + +
50C GLU 4.7 8.8 - - - +
51C GLU* 3.3 10.2 + - - +
52C VAL 3.3 0.2 - - - -
53C ALA* 1.3 79.8 - - - +
55C MET* 1.3 63.7 + - - +
57C LYS* 3.2 40.0 + - + +
58C ILE* 3.9 11.5 - - - +
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Residues in contact with MET 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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100B ALA* 5.2 9.2 - - + +
101B THR* 4.1 24.4 - - + +
104B ARG* 4.5 11.9 - - - +
19C LEU* 5.1 4.1 - - + +
21C HIS* 3.7 24.0 - - + +
44C VAL* 3.6 40.2 - - + -
46C ALA* 4.0 18.6 - - + -
51C GLU* 3.1 22.3 + - - +
52C VAL* 4.0 0.9 - - - +
53C ALA 3.3 0.2 - - - -
54C ASP* 1.3 76.0 - - - +
56C ALA* 1.3 65.5 + - - +
58C ILE* 3.2 33.6 - - - +
59C ALA* 3.3 8.8 + - - +
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Residues in contact with ALA 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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21C HIS* 3.5 16.5 + - - +
52C VAL 3.0 17.5 + - - +
53C ALA 4.1 2.5 - - - +
55C MET* 1.3 79.5 - - - +
57C LYS* 1.3 62.3 + - - +
58C ILE 3.2 0.9 + - - -
59C ALA* 3.2 15.6 + - - +
62C LEU* 4.2 13.2 - - + -
80C ALA* 3.6 26.0 - - + +
83C SER* 4.7 0.2 - - - -
84C ALA* 4.5 6.7 - - + +
89C VAL* 3.5 17.5 - - - +
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Residues in contact with LYS 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 ALA* 3.2 11.1 + - - +
54C ASP* 3.2 49.3 + - + +
56C ALA* 1.3 77.5 - - - +
58C ILE* 1.3 68.6 + - + +
59C ALA 4.5 0.2 - - - +
83C SER* 3.7 11.4 + - - +
87C HIS* 3.7 48.0 + - + +
89C VAL* 3.9 11.0 - - - +
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Residues in contact with ILE 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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100B ALA 5.5 7.0 - - - +
101B THR* 6.5 0.4 - - + -
19C LEU* 4.1 24.3 - - + +
54C ASP 3.9 8.7 - - - +
55C MET* 3.2 28.5 - - - +
57C LYS* 1.3 93.1 - - + +
59C ALA* 1.3 64.7 + - - +
60C GLY 4.0 0.2 + - - -
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Residues in contact with ALA 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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19C LEU* 3.8 18.8 - - + +
21C HIS* 3.8 16.4 - - + +
55C MET 3.3 12.7 + - - +
56C ALA* 3.2 13.2 + - - +
57C LYS 4.5 0.2 - - - +
58C ILE* 1.3 81.9 - - - +
60C GLY* 1.3 62.2 + - - +
61C ALA 3.7 20.4 - - - +
89C VAL* 3.4 20.0 - - + +
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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