Contacts of the helix formed by residues 99 - 104 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B ILE* 3.4 15.8 + - + +
95B ASN* 2.8 36.3 + - - +
97B ALA 3.4 0.2 - - - -
98B ALA* 1.3 77.4 - - + +
100B THR* 1.3 58.3 + - - +
101B TYR 3.6 1.3 - - - -
102B TYR* 3.4 5.5 + - - +
103B MET* 3.1 43.1 + - + +
140B PRO 5.2 3.6 - - - +
84D ASN* 5.0 0.2 + - - -
126D ALA* 3.2 32.0 + - + +
127D GLN* 4.4 3.4 - - + +
130D GLN* 2.8 30.8 + - - +
266D TRP* 3.8 25.7 - - + -
301D PRO* 4.1 23.1 - - + -
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Residues in contact with THR 100 (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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127A TYR* 3.8 17.2 + - - +
71B MET* 4.1 12.7 - - + +
95B ASN 4.4 0.5 + - - -
96B SER* 2.7 27.0 + - - -
97B ALA 3.4 7.2 + - - -
98B ALA 3.5 0.2 - - - -
99B LYS* 1.3 73.2 - - - +
101B TYR* 1.3 69.2 + - - +
102B TYR 3.0 1.8 + - - -
103B MET* 3.5 13.9 + - - +
104B SER* 3.1 19.1 + - - -
108B GLN* 3.3 37.0 - - + +
110B VAL* 4.1 6.5 - - + -
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Residues in contact with TYR 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A HIS* 3.3 24.9 - - - -
339A ILE 3.7 9.6 - - - +
340A TYR* 3.2 34.1 - - - -
341A SER* 3.5 23.0 + - - -
342A SER 4.8 0.9 + - - -
361A SER* 3.1 23.9 + - - -
97B ALA 4.6 3.0 + - - +
98B ALA 5.1 2.0 + - - +
100B THR* 1.3 78.6 - - - +
102B TYR* 1.3 59.6 + - - +
104B SER* 3.1 7.4 + - - -
106B GLY* 3.0 57.9 + - - -
108B GLN 3.3 12.5 + - - +
109B PRO* 3.6 31.0 - - + -
110B VAL* 4.9 2.8 - - + +
165B ASN* 5.6 1.6 - - - +
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Residues in contact with TYR 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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120A LYS* 3.4 33.3 - - + +
335A LEU 3.0 24.8 + - - -
336A GLY 4.6 0.2 - - - -
337A TYR 3.2 28.7 - - - -
338A HIS* 3.1 18.5 - - - +
339A ILE* 4.1 19.0 + - + +
98B ALA 5.6 1.1 + - - +
99B LYS* 3.4 5.9 + - - +
100B THR 3.0 0.8 - - - -
101B TYR* 1.3 75.9 - - - +
103B MET* 1.3 62.2 - - + +
104B SER 2.9 4.7 - - - -
105B GLY* 2.9 20.6 + - - -
300D VAL* 4.3 4.6 - - + +
301D PRO* 3.0 52.0 + - + -
302D MET 4.5 1.3 - - - -
303D PRO* 3.4 29.2 - - + +
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Residues in contact with MET 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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117A ALA* 3.5 15.1 - - - +
120A LYS* 4.8 3.6 - - - +
121A GLY* 3.6 19.4 + - - +
125A HIS* 3.6 46.1 - - + +
127A TYR* 4.1 7.6 - - - +
95B ASN 4.3 0.7 - - - +
99B LYS* 3.1 24.1 + - + +
100B THR* 3.5 20.8 + - - +
102B TYR* 1.3 78.8 - - + +
104B SER* 1.3 58.5 + - - +
105B GLY 3.1 2.0 + - - -
125D ALA* 6.2 0.2 - - + -
126D ALA* 3.5 32.5 - - + +
127D GLN* 3.6 28.9 - - - +
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Residues in contact with SER 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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116A CYS 4.9 0.9 - - - +
117A ALA* 4.0 12.1 - - - +
118A LYS* 4.8 0.2 + - - -
127A TYR* 3.3 35.7 - - - -
100B THR 3.1 10.8 + - - -
101B TYR 3.1 9.0 + - - -
102B TYR 2.9 1.4 - - - -
103B MET* 1.3 78.6 - - - +
105B GLY* 1.3 65.3 + - - +
107B LEU* 2.9 22.8 + - - +
108B GLN* 2.8 32.5 + - - -
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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