Contacts of the helix formed by residues 13 - 18 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G PHE* 3.2 11.8 + - + +
11G GLY 3.2 0.8 - - - -
12G GLU* 1.3 73.2 - - - +
14G ALA* 1.3 53.5 + - - +
15G PRO* 3.1 4.6 - - - +
16G TYR* 2.6 40.0 + - - +
17G LEU* 3.4 12.7 + - + +
133G PRO* 3.5 33.8 - - - +
134G VAL* 4.6 3.6 - - + -
136G ASN* 5.1 1.7 + - + +
139G VAL* 3.8 21.8 - - + -
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Residues in contact with ALA 14 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G MET* 3.2 31.3 - - + +
10G PHE* 3.7 7.2 - - + +
11G GLY* 2.8 29.4 + - - +
13G ALA* 1.3 75.4 - - - +
15G PRO* 1.3 55.0 - - + +
17G LEU* 2.9 3.4 + - - -
18G ARG 2.5 40.3 + - - +
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Residues in contact with PRO 15 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G GLY 3.3 4.3 - - - +
12G GLU* 3.2 16.4 - - - +
13G ALA 3.1 5.8 - - - -
14G ALA* 1.3 99.4 - - + +
16G TYR* 1.3 71.6 + - + +
17G LEU 3.4 0.2 - - - -
18G ARG 3.5 12.7 - - - +
19G MLY 3.9 37.4 + - - +
112G ALA 4.2 7.4 - - - +
114G MET* 4.3 3.5 - - - +
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Residues in contact with TYR 16 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G GLU 4.1 7.0 - - - -
13G ALA 2.6 25.3 + - - +
15G PRO* 1.3 87.2 - - + +
17G LEU* 1.3 60.6 + - - +
112G ALA 4.9 0.7 - - - -
113G TRP* 3.6 43.6 - + + +
114G MET* 3.3 21.2 - - - +
115G ILE* 4.4 4.0 + - - +
116G TYR* 5.5 1.9 + - - -
130G MLY 4.1 24.7 - - - -
131G TRP 5.9 0.2 - - - -
132G LEU* 4.4 13.9 - - + +
133G PRO* 3.2 43.1 - - + +
134G VAL* 4.2 16.8 - - + +
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Residues in contact with LEU 17 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G MET* 4.4 2.2 - - + -
10G PHE* 3.2 40.6 - - + -
13G ALA* 4.0 21.1 - - + +
14G ALA* 2.9 8.0 + - - +
16G TYR* 1.3 89.0 - - - +
18G ARG* 1.3 60.5 + - - +
89G GLU* 4.6 0.2 - - - +
109G ARG* 4.2 9.2 + - - -
114G MET* 3.9 13.1 - - - +
116G TYR* 5.2 4.8 - - + +
134G VAL* 4.3 23.8 - - + -
139G VAL* 4.7 4.3 - - + -
143G TYR* 4.0 21.5 - - + +
152G PRO* 3.6 24.9 - - + +
153G PRO* 4.9 12.7 - - - +
154G HIS* 5.0 2.9 - - + +
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Residues in contact with ARG 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6G GLU* 3.7 22.0 + - - -
7G MET* 3.3 33.9 - - + +
14G ALA 2.5 27.8 + - - +
15G PRO* 3.5 11.1 - - - +
17G LEU* 1.3 74.2 - - + +
19G MLY 1.3 68.8 + - - +
24G ARG* 4.7 24.1 - - - +
89G GLU* 2.9 40.0 + - - +
109G ARG* 6.0 0.4 - - - +
114G MET* 4.2 7.6 - - + -
149G GLN 4.8 9.3 + - - -
150G GLU 5.1 2.2 + - - -
151G ALA* 4.5 7.1 + - - +
152G PRO* 4.1 21.7 - - + +
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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