Contacts of the helix formed by residues 42 - 52 (chain C) in PDB entry 4OIP
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 VAL 42 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28C ARG* 3.9 36.1 - - + +
29C ALA 4.5 0.4 - - - +
31C GLN* 3.6 23.7 + - - +
40C GLU* 3.2 19.4 + - + +
41C ASN* 1.3 86.0 + - - +
43C GLY* 1.3 69.7 + - - +
44C ILE 3.4 0.2 + - - -
45C GLN* 3.1 11.8 + - - +
46C ALA* 3.1 14.9 + - - +
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Residues in contact with GLY 43 (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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29C ALA* 3.9 15.2 - - - +
42C VAL* 1.3 72.9 - - - +
44C ILE* 1.3 58.4 + - - -
46C ALA* 3.0 7.6 + - - +
47C ALA 2.9 22.3 + - - -
341C THR* 3.3 35.0 - - - +
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Residues in contact with ILE 44 (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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29C ALA 3.5 11.5 + - - +
30C LEU* 3.9 23.1 - - + +
42C VAL 3.4 0.4 + - - -
43C GLY* 1.3 70.0 - - - -
45C GLN* 1.3 62.9 + - - +
47C ALA* 3.2 9.1 + - - +
48C PHE* 2.9 37.3 + - + -
71C TYR* 3.5 37.5 - - + +
73C LEU* 4.8 3.4 - - + -
94C LEU* 5.2 3.8 - - + -
118C ILE* 4.7 10.3 - - + -
340C MET* 3.7 29.2 - - + -
341C THR* 4.0 1.3 + - - +
344C PHE* 3.7 33.4 - - + -
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Residues in contact with GLN 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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31C GLN* 3.8 13.7 - - - +
36C PRO 4.8 6.3 + - - +
39C ARG* 4.1 19.9 + - - +
40C GLU 3.4 17.9 - - - +
41C ASN* 4.1 9.4 - - - +
42C VAL 3.1 10.9 + - - +
44C ILE* 1.3 82.4 - - - +
46C ALA* 1.3 56.7 + - - +
48C PHE* 3.2 6.7 + - - +
49C ARG* 2.9 42.4 + - + +
68C PHE* 4.1 18.9 - - - -
69C LEU 5.4 2.2 + - - -
70C GLU* 5.5 1.3 - - - +
71C TYR* 3.0 32.3 + - + -
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Residues in contact with ALA 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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41C ASN* 3.1 24.1 + - - +
42C VAL* 3.1 23.0 + - - +
43C GLY 3.0 11.3 + - - +
45C GLN* 1.3 78.0 - - - +
47C ALA* 1.3 56.2 + - - +
49C ARG* 3.2 1.7 + - - +
50C GLU* 2.9 41.8 + - + +
288C ARG* 6.3 1.3 - - - +
345C ARG* 4.4 10.5 - - - +
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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 GLY 2.9 11.0 + - - +
44C ILE* 3.2 9.1 + - - +
46C ALA* 1.3 77.0 - - - +
48C PHE* 1.3 56.0 + - - +
50C GLU* 3.3 2.2 + - - +
51C THR* 2.8 35.0 + - - -
341C THR* 4.6 3.6 - - + +
344C PHE* 3.5 27.6 - - + -
345C ARG* 4.2 31.6 - - + +
348C LEU* 3.7 6.5 - - + -
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Residues in contact with PHE 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 ILE* 2.9 28.8 + - + -
45C GLN* 3.5 7.2 - - - +
47C ALA* 1.3 75.6 - - - +
49C ARG* 1.3 62.3 + - - +
52C PHE* 3.1 54.8 + + - +
68C PHE* 3.7 29.5 - + + -
71C TYR* 4.0 29.6 - + + -
94C LEU* 4.3 7.2 - - + -
96C ALA* 4.0 17.9 - - + -
115C LEU* 3.6 32.5 - - + -
344C PHE* 3.9 23.8 - + - -
348C LEU* 3.8 14.3 - - + +
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Residues in contact with ARG 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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41C ASN* 3.2 29.5 - - + +
45C GLN* 2.9 31.6 + - - +
46C ALA 3.2 7.8 + - - +
48C PHE* 1.3 77.1 - - - +
50C GLU* 1.3 59.2 + - + +
52C PHE* 2.8 22.4 + - - +
53C PRO* 6.1 1.0 - - - +
68C PHE* 4.2 20.9 - - - -
265C ARG* 5.1 1.4 + - - -
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Residues in contact with GLU 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 ALA* 2.9 22.2 + - + +
47C ALA* 3.8 4.5 - - - +
49C ARG* 1.3 78.4 - - + +
51C THR* 1.3 60.6 + - - +
52C PHE 3.2 0.6 + - - -
168C ARG* 3.2 25.8 + - - -
264C PRO 4.8 7.1 - - - +
265C ARG* 3.0 48.4 + - + +
268C ASP* 4.8 9.1 - - - +
288C ARG* 4.9 10.1 + - - +
345C ARG* 3.2 35.6 + - + +
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Residues in contact with THR 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 21.9 + - - -
50C GLU* 1.3 78.4 - - - +
52C PHE* 1.3 70.5 + - + +
54C ILE* 3.5 17.0 - - + +
265C ARG* 3.2 13.9 + - - +
345C ARG* 4.5 5.7 + - - +
348C LEU* 3.3 54.8 - - + +
349C ALA* 4.3 4.3 + - - +
351C LEU* 5.2 0.9 - - + -
352C ALA* 3.7 18.6 - - + +
356C ARG* 5.6 0.5 + - - -
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Residues in contact with PHE 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 PHE* 3.1 49.1 + + - +
49C ARG* 2.8 24.4 + - - +
50C GLU 3.9 2.1 - - - +
51C THR* 1.3 91.1 - - + +
53C PRO* 1.3 63.8 - - + +
54C ILE* 3.7 26.2 - - + -
66C LEU* 3.3 38.1 - - + -
67C ASP* 4.0 7.9 - - - +
68C PHE* 3.6 27.1 - - + +
98C LEU* 4.0 23.6 - - + -
265C ARG* 4.0 5.1 + - - -
348C LEU* 5.0 4.0 - - + -
351C LEU* 4.7 13.0 - - + -
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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