Contacts of the helix formed by residues 99 - 104 (chain V) in PDB entry 3EXG
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 LYS 99 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94V ILE* 3.3 20.7 + - - +
95V ASN* 3.0 37.9 + - - +
97V ALA 3.0 2.4 + - - -
98V ALA* 1.3 76.0 - - + +
100V THR* 1.3 64.0 + - - +
101V TYR 3.4 0.7 - - - -
102V TYR* 3.3 6.0 + - - +
103V MET* 3.1 35.7 + - + +
140V PRO 5.1 3.4 - - - +
84X ASN* 4.9 0.2 + - - -
126X ALA 3.1 30.2 + - - +
127X GLN* 4.3 3.2 - - + +
130X GLN* 2.8 34.4 + - - +
266X TRP* 4.0 19.6 - - - -
301X PRO* 3.9 24.2 - - + -
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Residues in contact with THR 100 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127U TYR* 4.2 10.1 + - + -
71V MET* 4.3 11.1 - - + +
95V ASN 4.5 0.7 + - - -
96V SER* 3.0 27.4 + - - -
97V ALA 3.0 8.2 + - - -
99V LYS* 1.3 75.8 - - - +
101V TYR* 1.3 70.9 + - - +
103V MET* 4.0 17.5 - - - +
104V SER* 3.2 18.5 + - - -
108V GLN* 3.3 39.0 - - + +
110V VAL* 3.9 8.1 - - + -
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Residues in contact with TYR 101 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338U HIS* 3.7 13.0 + - - -
339U ILE 3.7 14.6 - - - +
340U TYR 3.2 35.7 - - - -
341U SER* 3.4 25.3 + - - -
342U SER 4.6 0.3 + - - -
361U SER* 3.4 25.4 + - - -
97V ALA 4.4 1.4 + - - -
98V ALA 4.4 3.6 + - - +
99V LYS 3.3 0.8 + - - -
100V THR* 1.3 77.9 - - - +
102V TYR* 1.3 60.7 + - - +
104V SER* 3.0 8.9 + - - -
106V GLY* 3.0 61.3 + - - -
108V GLN 3.2 25.1 + - - +
109V PRO* 3.6 15.9 - - + -
110V VAL* 5.0 2.8 - - + +
165V ASN* 5.1 3.6 - - - +
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Residues in contact with TYR 102 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120U LYS* 3.4 37.1 + - + +
335U LEU* 2.9 31.6 + - - +
336U GLY* 4.7 3.1 - - - -
337U TYR 3.2 23.8 - - - -
338U HIS* 3.0 17.9 + - - +
339U ILE* 4.3 13.8 + - + +
98V ALA 5.5 0.9 - - - +
99V LYS 3.3 3.7 + - - +
100V THR 3.2 0.2 - - - -
101V TYR* 1.3 76.8 - - - +
103V MET* 1.3 69.1 - - + +
105V GLY* 3.0 14.7 + - - -
141V GLY* 6.5 0.2 - - - -
300X VAL* 4.4 5.9 - - + +
301X PRO* 2.7 60.5 + - + -
302X MET 4.3 1.6 - - - -
303X PRO* 3.6 25.1 - - + +
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Residues in contact with MET 103 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117U ALA* 3.6 14.6 - - - +
120U LYS* 4.1 10.3 - - - +
121U GLY* 3.7 13.7 + - - -
125U HIS* 3.6 45.1 - - + +
127U TYR* 3.6 20.4 - - - +
95V ASN 4.3 1.3 - - - +
99V LYS* 3.1 19.4 + - + +
100V THR* 4.0 22.2 - - - +
102V TYR* 1.3 79.8 - - + +
104V SER* 1.3 57.8 + - - +
105V GLY 3.3 1.2 + - - -
126X ALA* 3.6 32.8 - - + -
127X GLN* 3.8 23.6 - - + +
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Residues in contact with SER 104 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116U CYS 4.3 0.9 - - - +
117U ALA* 3.9 16.0 - - - +
118U LYS* 5.0 0.2 + - - -
127U TYR* 3.3 38.8 - - - -
100V THR 3.2 9.8 + - - -
101V TYR 3.0 11.4 + - - -
102V TYR 3.1 1.2 - - - -
103V MET* 1.3 76.4 - - - +
105V GLY* 1.3 60.9 + - - +
106V GLY 3.3 0.2 + - - -
107V LEU* 3.1 24.2 + - - +
108V GLN* 3.1 23.2 + - - -
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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