Contacts of the helix formed by residues 101 - 106 (chain B) in PDB entry 1OE4
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 101 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98B GLY* 3.3 6.5 + - - -
99B PRO 3.5 0.2 - - - -
100B PHE* 1.3 76.5 - - - +
102B MET* 1.3 60.4 + - - -
103B ALA 3.1 0.4 - - - -
104B GLN* 2.9 22.3 + - - +
105B THR* 3.0 12.0 + - - -
109B PHE* 5.7 0.2 - - - -
110B GLY 3.4 26.4 - - - +
111B GLU 4.0 0.2 - - - -
146B GLU* 3.5 19.2 + - - -
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Residues in contact with MET 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B GLU* 5.8 0.2 - - - +
68B PRO* 3.4 16.2 - - + +
69B LEU* 3.6 38.8 - - + -
76B HIS* 4.6 5.4 - - + +
97B PRO* 3.7 24.2 - - + -
98B GLY 3.8 5.0 + - - +
101B GLY* 1.3 71.4 - - - -
103B ALA* 1.3 59.3 + - - +
105B THR* 3.8 3.6 - - - -
106B GLY* 2.9 28.8 + - - +
107B VAL 3.1 24.5 - - - +
108B PRO* 3.7 20.4 - - + -
109B PHE* 4.5 2.8 - - - +
110B GLY 3.7 6.5 - - - +
174B ASN* 3.3 28.9 - - + +
177B PRO* 5.0 6.5 - - + -
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Residues in contact with ALA 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B TYR* 5.1 1.1 - - + -
68B PRO* 4.2 6.3 - - - -
71B TYR* 2.6 42.6 + - - +
97B PRO* 4.0 3.2 - - + +
98B GLY 3.3 19.0 + - - +
99B PRO* 3.5 19.3 - - + +
101B GLY 3.1 1.2 + - - -
102B MET* 1.3 78.9 - - - +
104B GLN* 1.3 57.5 + - - +
137B ILE* 3.4 10.8 - - + +
179B ILE* 4.3 17.9 - - + -
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Residues in contact with GLN 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ALA* 4.9 1.1 - - - -
99B PRO 3.0 18.1 + - - +
100B PHE* 3.5 30.4 - - - +
101B GLY 2.9 5.9 + - - +
103B ALA* 1.3 79.2 - - - +
105B THR* 1.3 63.2 + - + +
106B GLY 3.7 0.7 - - - -
112B VAL* 4.7 0.4 - - + -
125B VAL* 3.7 16.2 - - - +
135B ARG 5.7 0.6 - - - -
136B ARG 3.3 19.4 + - - -
137B ILE* 3.4 14.0 - - - +
138B ARG 2.8 27.8 + - - -
139B GLY* 3.1 38.7 + - - +
142B CYS* 3.7 23.3 - - + +
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Residues in contact with THR 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ALA* 4.2 0.9 - - - -
75B PRO* 3.2 30.5 - - - +
101B GLY 3.0 6.0 + - - +
104B GLN* 1.3 78.4 - - - +
106B GLY* 1.3 61.0 + - - +
107B VAL* 3.2 15.7 + - - +
110B GLY* 2.8 34.9 + - - +
112B VAL* 3.8 27.1 - - + -
115B VAL* 4.4 7.0 - - + -
139B GLY 5.1 0.4 - - - +
140B PHE* 4.0 31.4 - - + -
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Residues in contact with GLY 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B PRO* 4.5 5.2 - - - -
69B LEU* 4.1 0.6 - - - +
72B ALA* 3.7 25.2 - - - +
76B HIS* 2.8 36.8 + - - +
102B MET* 2.9 27.7 + - - +
104B GLN 3.7 0.6 - - - -
105B THR* 1.3 76.3 - - - +
107B VAL* 1.3 56.0 + - - +
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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