Contacts of the helix formed by residues 99 - 104 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94J ILE* 3.4 21.4 + - - +
95J ASN* 2.9 31.3 + - - +
96J SER 4.5 0.6 + - - -
97J ALA 3.3 0.4 - - - -
98J ALA* 1.3 80.9 - - + +
100J THR* 1.3 65.7 + - - +
101J TYR 3.2 2.0 + - - -
102J TYR* 3.4 7.7 + - - +
103J MET* 3.0 36.0 + - + +
140J PRO 5.0 3.4 - - - +
84L ASN* 5.4 0.2 + - - -
126L ALA* 3.0 29.4 + - + +
127L GLN* 4.1 3.4 + - + +
130L GLN* 2.8 32.4 + - - +
266L TRP* 3.9 18.7 - - - -
301L PRO* 3.7 25.8 - - + -
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Residues in contact with THR 100 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127I TYR* 3.6 17.1 + - + +
135I ASN* 5.7 1.2 + - - -
71J MET* 4.0 13.8 - - + +
96J SER* 2.7 26.9 + - - -
97J ALA 3.6 5.6 + - - -
98J ALA 3.5 1.8 - - - -
99J LYS* 1.3 76.6 - - - +
101J TYR* 1.3 65.4 + - - +
103J MET* 3.1 15.0 + - - +
104J SER* 2.9 21.7 + - - -
108J GLN* 3.4 37.7 - - + +
110J VAL* 4.1 6.1 - - + -
127L GLN* 5.5 0.2 + - - -
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Residues in contact with TYR 101 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338I HIS* 3.2 29.4 - - + -
339I ILE 3.6 15.7 - - - +
340I TYR 3.4 22.9 - - - -
341I SER* 3.5 22.9 - - - -
342I SER 5.1 0.2 + - - -
361I SER* 3.1 22.6 + - - -
97J ALA 4.7 3.0 + - - +
98J ALA 4.9 2.0 + - - +
99J LYS 3.2 1.0 + - - -
100J THR* 1.3 75.1 - - - +
102J TYR* 1.3 65.1 + - - +
104J SER* 3.0 15.5 + - - -
106J GLY* 3.0 45.8 + - - -
108J GLN 3.4 24.0 + - - +
109J PRO* 3.6 19.3 - - + -
110J VAL* 5.2 2.6 - - + +
165J ASN* 5.1 2.9 - - - +
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Residues in contact with TYR 102 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120I LYS* 3.7 35.4 + - + +
335I LEU* 2.8 31.6 + - - +
337I TYR 3.7 21.1 - - - -
338I HIS* 3.1 18.0 + - - +
339I ILE* 3.8 24.8 + - + +
98J ALA 5.5 1.5 + - - +
99J LYS* 3.4 9.4 + - - +
101J TYR* 1.3 78.5 - - - +
103J MET* 1.3 65.5 + - + +
105J GLY* 2.9 20.4 + - - -
300L VAL* 4.2 8.0 - - + +
301L PRO* 2.8 45.5 + - + -
302L MET 5.1 0.7 - - - -
303L PRO* 3.8 24.9 - - + +
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Residues in contact with MET 103 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117I ALA* 3.5 14.1 - - - +
120I LYS* 4.5 7.0 - - - +
121I GLY* 3.7 16.8 + - - -
125I HIS* 3.3 53.6 - - + +
127I TYR* 3.7 14.6 - - - +
95J ASN 4.2 2.7 - - - +
99J LYS* 3.0 14.5 + - + +
100J THR* 3.1 26.2 + - - +
102J TYR* 1.3 79.2 - - + +
104J SER* 1.3 58.9 + - - +
105J GLY 3.1 1.5 + - - -
125L ALA* 6.0 0.2 - - + -
126L ALA* 3.6 33.0 - - + +
127L GLN* 3.9 19.1 - - - +
302L MET 5.6 0.2 - - - +
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Residues in contact with SER 104 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116I CYS 4.7 0.5 - - - +
117I ALA* 3.8 12.4 - - - +
127I TYR* 3.3 39.0 - - - -
100J THR 2.9 11.4 + - - -
101J TYR 3.0 11.4 + - - -
102J TYR 3.1 0.2 - - - -
103J MET* 1.3 77.2 - - - +
105J GLY* 1.3 63.4 + - - +
107J LEU* 3.0 33.6 + - - +
108J GLN* 3.1 14.9 + - - +
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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