Contacts of the helix formed by residues 13 - 18 (chain A) in PDB entry 1O1F
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 ALA 13 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A PHE* 3.2 11.2 + - + +
11A GLY 3.2 0.6 - - - -
12A GLU* 1.3 73.7 - - - +
14A ALA* 1.3 54.1 - - - +
15A PRO* 3.1 4.8 - - - +
16A TYR* 2.6 40.2 + - - +
17A LEU* 3.4 13.0 + - + +
133A PRO* 3.5 34.5 - - + +
134A VAL* 4.6 3.1 - - + -
136A ASN* 5.1 1.5 + - + +
138A MLY 6.2 0.2 - - + -
139A VAL* 3.8 21.3 - - + -
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Residues in contact with ALA 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A MET* 3.2 31.8 - - + +
10A PHE* 3.7 7.4 - - + +
11A GLY* 2.8 28.2 + - - +
13A ALA* 1.3 75.4 - - - +
15A PRO* 1.3 57.2 - - + +
17A LEU* 2.9 3.5 + - - -
18A ARG 2.5 40.5 + - - +
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Residues in contact with PRO 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A GLY 3.3 4.9 - - - +
12A GLU* 3.2 15.3 - - - +
13A ALA 3.1 7.0 - - - +
14A ALA* 1.3 95.9 - - + +
16A TYR* 1.3 72.9 + - + +
18A ARG 3.5 12.2 - - - +
19A MLY 3.9 37.3 + - - +
112A ALA 4.2 7.4 - - - +
114A MET* 4.3 3.5 - - - +
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Residues in contact with TYR 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A GLU 4.1 7.2 - - - -
13A ALA 2.6 24.8 + - - +
15A PRO* 1.3 85.8 - - + +
17A LEU* 1.3 61.9 + - - +
112A ALA 4.9 0.4 - - - -
113A TRP* 3.6 41.8 - + + +
114A MET* 3.3 23.1 - - - +
115A ILE* 4.4 3.8 + - - +
116A TYR* 5.5 2.1 + - - -
130A MLY 4.1 24.7 - - - -
131A TRP 5.9 0.2 - - - -
132A LEU* 4.4 13.0 - - + -
133A PRO* 3.2 42.4 - - + +
134A VAL* 4.2 16.4 - - + +
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Residues in contact with LEU 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A MET* 4.4 1.8 - - + -
10A PHE* 3.2 40.4 - - + -
13A ALA* 4.0 19.5 - - + +
14A ALA* 3.5 7.6 - - - +
16A TYR* 1.3 88.4 - - - +
18A ARG* 1.3 60.9 + - - +
109A ARG* 4.2 9.5 + - - -
114A MET* 3.9 13.3 - - - +
116A TYR* 5.2 4.8 - - + +
134A VAL* 4.3 22.9 - - + -
139A VAL* 4.7 4.9 - - + -
143A TYR* 4.0 20.2 - - + +
152A PRO* 3.6 24.5 - - + +
153A PRO* 4.9 12.1 - - - +
154A HIS* 5.0 3.6 - - + +
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Residues in contact with ARG 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A GLU* 3.7 21.4 + - - -
7A MET* 3.3 34.5 - - + +
14A ALA 2.5 27.8 + - - +
15A PRO* 3.5 10.4 - - - +
17A LEU* 1.3 74.0 - - + +
19A MLY 1.3 69.8 + - - +
24A ARG* 4.7 23.5 - - - +
89A GLU* 2.9 40.0 + - - +
109A ARG* 6.0 0.7 - - - +
114A MET* 4.2 6.3 - - + -
149A GLN 4.8 9.9 + - - -
150A GLU 5.1 2.2 + - - -
151A ALA* 4.5 6.9 - - - +
152A PRO* 4.1 21.3 - - + +
722A GLN* 6.0 3.0 - - - +
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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