Contacts of the helix formed by residues 99 - 104 (chain Z) 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 Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1262 ALA* 3.2 27.7 + - + +
1272 GLN* 4.5 1.5 - - + +
1302 GLN* 2.8 33.5 + - - +
2662 TRP* 3.7 23.4 - - - -
3012 PRO* 3.7 25.7 - - + +
94Z ILE* 3.4 22.8 + - - +
95Z ASN* 3.3 34.6 + - - +
97Z ALA 3.3 0.6 - - - -
98Z ALA* 1.3 81.3 - - + +
100Z THR* 1.3 64.0 + - - +
101Z TYR 3.5 0.2 - - - -
102Z TYR* 3.4 5.8 + - - +
103Z MET* 3.0 38.4 + - + +
139Z CYS* 6.3 0.7 - - - -
140Z PRO 5.3 4.0 - - - +
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Residues in contact with THR 100 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127Y TYR* 3.8 19.3 + - + +
71Z MET* 4.6 6.4 - - + +
95Z ASN 4.1 2.6 + - - -
96Z SER* 2.7 31.2 + - - +
97Z ALA 3.5 0.2 + - - -
98Z ALA 3.3 2.0 - - - -
99Z LYS* 1.3 75.8 - - - +
101Z TYR* 1.3 72.1 + - - +
103Z MET* 3.2 9.7 + - - +
104Z SER* 3.1 19.1 + - - -
108Z GLN* 3.4 37.5 - - + +
110Z VAL* 3.9 12.6 - - + -
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Residues in contact with TYR 101 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338Y HIS* 3.3 22.0 - - - -
339Y ILE 3.7 9.0 - - - +
340Y TYR 3.0 31.0 - - - -
341Y SER* 3.7 21.7 + - - -
342Y SER 4.9 0.5 + - - -
361Y SER* 2.8 24.1 + - - -
97Z ALA 4.5 2.4 + - - +
98Z ALA 4.3 4.1 + - - +
99Z LYS 3.5 0.4 - - - -
100Z THR* 1.3 81.5 - - - +
102Z TYR* 1.3 62.7 + - - +
104Z SER* 2.9 15.6 + - - -
106Z GLY* 3.2 46.3 + - - -
108Z GLN 3.3 22.6 + - - +
109Z PRO* 3.4 25.6 - - + -
110Z VAL* 4.7 2.6 - - + +
165Z ASN* 4.7 4.9 - - - +
166Z PRO* 6.4 2.0 - - + -
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Residues in contact with TYR 102 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3002 VAL* 4.2 10.3 - - + +
3012 PRO* 2.8 53.6 + - + -
3022 MET 4.4 1.1 - - - -
3032 PRO* 3.3 36.8 - - + +
120Y LYS* 3.4 34.7 + - + +
335Y LEU* 3.0 28.5 + - - +
337Y TYR 3.4 15.5 - - - -
338Y HIS* 3.0 19.6 + - - +
339Y ILE* 4.1 19.6 + - + +
98Z ALA 5.0 1.3 + - - +
99Z LYS* 3.4 3.4 + - - +
100Z THR 3.3 0.2 - - - -
101Z TYR* 1.3 78.8 - - - +
103Z MET* 1.3 68.8 + - + +
104Z SER 3.3 0.7 + - - -
105Z GLY* 3.3 9.0 + - - -
141Z GLY* 6.4 0.2 - - - -
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Residues in contact with MET 103 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1262 ALA* 3.7 30.7 - - + +
1272 GLN* 3.7 28.9 - - + +
117Y ALA* 3.7 14.0 - - - +
120Y LYS* 4.2 9.3 - - - +
121Y GLY* 3.8 13.8 + - - -
125Y HIS* 3.3 50.2 - - + +
127Y TYR* 3.9 15.9 - - - +
95Z ASN 4.0 8.3 - - - +
99Z LYS* 3.0 30.7 + - + +
100Z THR* 3.2 6.5 + - - +
102Z TYR* 1.3 79.7 - - + +
104Z SER* 1.3 59.7 + - - +
105Z GLY 3.2 1.1 - - - -
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Residues in contact with SER 104 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117Y ALA* 3.9 13.6 - - - +
127Y TYR* 3.4 32.2 - - - +
100Z THR 3.1 11.3 + - - -
101Z TYR 2.9 11.5 + - - -
103Z MET* 1.3 77.3 - - - +
105Z GLY* 1.3 62.3 + - - +
107Z LEU* 2.9 24.1 + - - +
108Z GLN* 2.8 35.8 + - - -
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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