Contacts of the helix formed by residues 44 - 52 (chain C) in PDB entry 4IXU
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 HIS 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 GLY* 2.8 20.8 + - - +
43C GLU* 1.3 99.9 + - + +
45C GLY* 1.3 62.9 + - - +
46C PRO 3.4 2.0 - - - -
47C ALA* 3.3 12.8 + - + +
48C ALA* 3.0 22.3 + - - +
299C PRO* 3.9 15.3 - - + -
300C GLN* 3.1 31.1 + - + -
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Residues in contact with GLY 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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42C VAL 3.1 7.0 + - - -
44C HIS* 1.3 76.9 - - - +
46C PRO* 1.3 68.1 - - - +
48C ALA* 3.2 2.3 + - - +
49C ILE* 2.9 29.9 + - - +
117C GLY 3.5 9.9 - - - -
297C VAL* 3.3 28.3 + - - -
299C PRO* 3.9 5.5 - - - +
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Residues in contact with PRO 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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30C GLY* 4.0 2.7 - - - -
31C ALA 4.0 8.3 - - - +
32C PRO* 4.1 9.6 - - + -
43C GLU 3.4 15.0 - - - +
44C HIS 3.5 1.1 - - - -
45C GLY* 1.3 89.4 - - - +
47C ALA* 1.3 55.7 + - - +
49C ILE* 3.3 2.3 + - - +
50C ARG* 2.9 35.4 + - - +
70C ASP* 3.6 24.0 - - - +
116C LEU* 3.4 44.9 - - + +
117C GLY 3.2 12.5 - - - +
118C GLY 3.8 1.3 - - - +
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Residues in contact with ALA 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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43C GLU 5.8 0.2 - - - +
44C HIS* 3.3 16.2 + - + +
45C GLY 3.2 0.6 - - - -
46C PRO* 1.3 80.6 - - - +
48C ALA* 1.3 58.5 + - - +
50C ARG* 3.3 10.8 + - - +
51C GLU* 2.8 46.3 + - + +
70C ASP* 4.3 8.6 + - - +
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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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44C HIS 3.0 13.8 + - - +
45C GLY* 3.6 8.5 - - - +
47C ALA* 1.3 75.6 - - - +
49C ILE* 1.3 58.9 + - - +
51C GLU* 3.4 14.2 + - - +
52C ALA* 3.0 22.2 + - - +
297C VAL* 4.7 4.5 - - + -
299C PRO* 3.9 24.5 - - + -
308C ALA 5.7 1.1 - - - +
312C ALA* 3.5 24.6 - - + +
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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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45C GLY 2.9 24.4 + - - +
46C PRO 3.7 3.4 - - - +
48C ALA* 1.3 73.9 - - - +
50C ARG* 1.3 66.8 + - - +
52C ALA* 3.1 12.5 + - - -
54C LEU* 3.6 14.6 + - + -
116C LEU* 4.0 35.0 - - + -
117C GLY 4.5 1.8 - - - +
294C LEU* 4.0 21.1 - - + +
297C VAL* 4.2 15.3 - - + -
312C ALA* 4.5 2.7 - - - +
315C ALA* 3.9 26.0 - - + -
316C VAL* 3.4 29.7 - - + +
319C ILE* 4.3 6.3 - - + -
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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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28C VAL* 4.2 15.3 + - - +
30C GLY* 3.8 9.5 - - - +
46C PRO 2.9 21.6 + - - +
47C ALA* 3.6 8.3 - - - +
49C ILE* 1.3 78.3 - - - +
51C GLU* 1.3 57.8 + - + +
53C GLY* 2.9 21.7 + - - -
54C LEU* 3.7 9.8 + - + -
55C MET* 4.5 16.6 + - + +
67C ASP* 2.7 43.8 + - - -
69C GLY* 3.3 28.1 + - - -
70C ASP* 3.1 19.5 + - - -
116C LEU* 4.4 11.3 - - + +
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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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47C ALA* 2.8 35.0 + - + +
48C ALA* 3.7 12.5 - - - +
49C ILE 3.3 0.2 - - - -
50C ARG* 1.3 76.9 - - + +
52C ALA* 1.3 58.3 + - - +
53C GLY* 3.0 4.4 + - - -
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Residues in contact with ALA 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 3.0 13.3 + - - +
49C ILE 3.5 10.1 - - - +
50C ARG 3.1 1.0 - - - -
51C GLU* 1.3 74.9 - - - +
53C GLY* 1.3 58.2 + - - +
54C LEU 3.7 1.3 - - - -
57C ARG* 5.1 4.0 + - - +
312C ALA* 3.8 15.9 - - + +
313C ASN* 3.4 26.3 - - - +
316C VAL* 3.6 22.3 - - + +
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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
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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