Contacts of the helix formed by residues 17 - 25 (chain C) in PDB entry 1OJ7
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 GLY 17 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3B ASN* 4.3 1.9 + - - -
16C LYS* 1.3 75.5 - - - +
18C ALA* 1.3 56.5 + - - +
19C ILE* 3.1 13.8 - - - +
20C ALA* 3.0 28.8 + - - +
49C GLN* 5.7 2.5 - - - -
176C ASP* 2.9 15.3 + - - -
179C TYR* 5.6 0.2 - - - -
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Residues in contact with ALA 18 (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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3B ASN* 4.3 7.6 - - + +
13C LEU* 3.7 38.4 - - + +
14C PHE 3.7 6.3 - - - +
15C GLY 3.0 27.3 + - - +
16C LYS 3.3 1.0 - - - -
17C GLY* 1.3 72.0 - - - +
19C ILE* 1.3 59.5 + - - +
20C ALA 3.0 5.8 - - - -
21C GLY* 3.1 15.7 + - - +
174C VAL* 3.9 9.4 - - + -
175C LEU 4.9 0.2 - - - +
176C ASP* 4.1 2.4 + - - -
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Residues in contact with ILE 19 (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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17C GLY* 4.2 9.6 - - - +
18C ALA* 1.3 76.9 - - - +
20C ALA* 1.3 64.1 + - - +
21C GLY 3.0 0.4 - - - -
22C LEU* 3.0 34.8 + - + +
49C GLN* 3.4 54.1 - - + +
50C VAL* 4.6 5.2 - - + -
53C ALA* 3.8 11.9 - - + +
136C VAL* 4.0 22.7 - - + -
174C VAL* 3.8 20.4 - - + +
176C ASP* 5.3 0.2 + - - -
179C TYR* 3.4 22.7 - - + +
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Residues in contact with ALA 20 (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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340A PRO* 6.3 3.6 - - + -
17C GLY 3.0 15.8 + - - +
18C ALA 3.0 1.4 - - - -
19C ILE* 1.3 79.0 - - - +
21C GLY* 1.3 58.7 + - - +
22C LEU 3.3 1.0 + - - -
23C ARG* 4.6 6.8 + - - +
24C GLU* 4.7 4.9 + - - +
53C ALA* 5.3 3.9 - - - +
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Residues in contact with GLY 21 (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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13C LEU* 3.8 12.7 - - - +
18C ALA 3.1 10.9 + - - -
19C ILE 3.0 1.4 - - - -
20C ALA* 1.3 77.5 - - - +
22C LEU* 1.3 62.9 + - - +
23C ARG 3.3 2.0 - - - -
24C GLU* 3.3 23.0 + - - +
25C GLN* 3.4 17.4 + - - +
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Residues in contact with LEU 22 (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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13C LEU* 4.3 1.9 - - - +
19C ILE* 3.0 34.3 + - + +
20C ALA 3.3 0.6 - - - -
21C GLY* 1.3 76.5 - - - +
23C ARG* 1.3 60.4 + - - +
25C GLN* 2.9 23.0 + - - +
26C ILE* 3.3 19.3 + - + +
50C VAL* 4.0 15.0 - - + -
53C ALA* 4.3 11.0 - - + -
54C LEU* 4.2 15.7 - - + -
90C LEU* 3.8 30.7 - - + -
136C VAL* 4.6 2.9 - - + -
172C PHE* 3.4 38.6 - - + -
174C VAL* 4.2 10.3 - - + -
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Residues in contact with ARG 23 (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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185A PRO* 3.4 45.8 - - + +
232A LEU 5.2 1.4 + - - -
235A PRO* 6.2 1.0 - - - +
20C ALA 4.6 5.8 + - - +
21C GLY 3.3 0.8 - - - -
22C LEU* 1.3 80.4 - - - +
24C GLU* 1.3 61.2 + - + +
26C ILE* 3.2 24.2 + - - +
28C HIS* 3.1 50.3 + - - +
53C ALA* 3.9 22.4 - - - +
54C LEU* 4.5 4.3 - - - +
55C LYS 3.5 20.6 + - - -
56C GLY* 4.7 4.4 + - - -
57C MET* 3.2 38.4 - - - +
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Residues in contact with GLU 24 (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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184A PRO* 6.1 4.7 - - + -
186A ARG* 3.6 45.0 + - + +
20C ALA 4.7 3.6 - - - +
21C GLY* 3.3 18.3 + - - +
22C LEU 3.2 0.8 - - - -
23C ARG* 1.3 80.7 - - + +
25C GLN* 1.3 69.5 + - - +
26C ILE 3.6 1.7 - - - +
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Residues in contact with GLN 25 (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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5B ASN* 3.6 15.6 - - - +
11C ARG* 3.3 41.0 + - - +
13C LEU* 3.9 18.9 - - + +
21C GLY* 3.4 16.4 + - - +
22C LEU* 2.9 8.1 + - - +
24C GLU* 1.3 88.4 + - - +
26C ILE* 1.3 60.8 + - - +
27C PRO* 4.1 4.2 - - - +
88C PHE* 4.7 3.6 - - - -
171C VAL* 4.8 9.7 - - - +
172C PHE* 3.6 32.3 - - + +
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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