Contacts of the helix formed by residues 99 - 104 (chain G) in PDB entry 2Q9Q
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 PRO 99 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A ARG* 3.7 46.0 - - + +
94G TYR* 4.1 14.4 - - + -
97G ILE 4.0 5.4 - - - +
98G LEU* 1.3 82.6 - - + +
100G ASN* 1.3 66.5 + - - +
101G ALA* 4.3 4.9 - - + +
102G LEU* 2.8 42.9 + - + +
103G ARG 3.1 9.9 + - - -
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Residues in contact with ASN 100 (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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133A ASP* 5.7 2.0 - - - +
147D ARG* 6.0 3.4 - - - +
98G LEU 3.3 1.6 + - - -
99G PRO* 1.3 71.8 - - - +
101G ALA* 1.3 60.8 + - - +
103G ARG* 2.9 35.8 + - - +
104G PHE* 2.8 61.5 + - + -
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Residues in contact with ALA 101 (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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130A VAL* 4.3 9.9 - - + +
133A ASP* 3.8 24.8 + - + +
134A SER* 3.6 46.6 + - - +
137A ARG* 5.0 3.4 - - + -
147D ARG* 5.9 1.5 - - - +
99G PRO* 3.0 7.5 + - + +
100G ASN* 1.3 80.6 - - - +
102G LEU* 1.3 60.6 + - - +
104G PHE* 3.9 11.2 + - - +
105G HIS* 4.1 11.1 + - - -
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Residues in contact with LEU 102 (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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134A SER* 5.2 0.7 - - - +
137A ARG* 4.6 4.9 - - + -
138A GLN* 3.4 42.2 - - + +
21G LEU* 4.5 10.1 - - + +
90G LEU* 4.5 20.0 - - + -
94G TYR* 3.4 40.2 - - + -
98G LEU* 4.9 4.0 - - + -
99G PRO* 2.8 38.6 + - + +
101G ALA* 1.3 79.4 - - + +
103G ARG* 1.3 65.2 + - + +
104G PHE 3.2 0.4 - - - -
105G HIS* 3.2 21.6 + - - +
106G MET* 3.7 11.7 - - - +
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Residues in contact with ARG 103 (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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97G ILE* 4.8 9.0 - - - +
98G LEU* 3.0 45.6 + - + +
99G PRO 3.1 11.2 + - - +
100G ASN* 2.9 32.6 + - - +
102G LEU* 1.3 76.2 - - - +
104G PHE* 1.3 68.6 + - + +
105G HIS 3.1 0.2 - - - -
106G MET* 3.0 35.0 + - - +
111G MET* 3.4 31.0 - - + +
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Residues in contact with PHE 104 (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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82A GLU* 3.8 22.0 - - - +
130A VAL* 4.4 24.9 - - + -
147D ARG* 6.0 2.9 - - - -
100G ASN* 2.8 53.7 + - + +
101G ALA 4.3 5.6 - - - +
102G LEU 3.2 0.8 - - - -
103G ARG* 1.3 86.9 - - + +
105G HIS* 1.3 62.1 + - + +
106G MET 3.3 4.8 - - - +
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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