Contacts of the helix formed by residues 99 - 104 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84B ASN* 5.3 0.2 + - - -
126B ALA* 3.5 28.6 + - + +
127B GLN* 4.5 1.9 - - + +
130B GLN* 2.9 28.3 + - - +
266B TRP* 3.8 26.3 - - - -
301B PRO* 3.8 24.5 - - + -
94D ILE* 3.3 20.1 + - - +
95D ASN* 3.1 32.0 + - - +
97D ALA 3.5 0.2 - - - -
98D ALA* 1.3 79.3 - - + +
100D THR* 1.3 63.7 + - - +
101D TYR 3.4 0.7 - - - -
102D TYR* 3.3 7.0 + - - +
103D MET* 3.0 36.4 + - + +
139D CYS* 6.4 0.2 - - - -
140D PRO 5.0 3.1 - - - +
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Residues in contact with THR 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B GLN* 5.3 0.2 + - - -
127C TYR* 3.6 22.5 + - + +
71D MET* 4.4 6.0 - - + +
95D ASN 4.1 0.2 + - - -
96D SER* 2.5 31.7 + - - +
97D ALA 3.4 4.2 + - - -
98D ALA 3.3 2.0 - - - -
99D LYS* 1.3 76.0 - - - +
101D TYR* 1.3 69.6 + - - +
103D MET* 3.9 13.5 - - - +
104D SER* 3.1 19.1 + - - -
108D GLN* 3.4 35.0 - - + +
110D VAL* 4.1 7.6 - - + -
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Residues in contact with TYR 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338C HIS* 3.1 23.1 - - - +
339C ILE 3.6 11.9 - - - +
340C TYR 3.2 35.7 - - - -
341C SER* 3.2 25.3 - - - -
342C SER 4.9 0.2 + - - -
361C SER 2.9 24.5 + - - -
97D ALA 4.5 2.6 + - - +
98D ALA 4.3 3.6 + - - +
99D LYS 3.4 0.8 - - - -
100D THR* 1.3 81.5 - - - +
102D TYR* 1.3 60.6 + - - +
104D SER* 3.0 13.7 + - - -
106D GLY* 3.1 48.0 + - - -
108D GLN 3.5 23.0 + - - +
109D PRO* 3.6 15.3 - - + -
110D VAL* 5.0 2.4 - - + +
165D ASN* 4.7 4.3 - - - +
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Residues in contact with TYR 102 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300B VAL* 4.2 14.2 - - + +
301B PRO* 3.2 47.0 + - + -
302B MET 4.4 1.1 - - - -
303B PRO* 3.4 35.4 - - + +
120C LYS* 3.6 30.9 - - + +
335C LEU* 2.8 30.8 + - - +
336C GLY 4.5 1.1 - - - -
337C TYR 3.3 24.9 - - - -
338C HIS* 2.9 19.6 + - - +
339C ILE* 4.1 13.0 + - + +
98D ALA 5.1 1.1 + - - +
99D LYS* 3.3 7.7 + - - +
100D THR 3.1 0.4 - - - -
101D TYR* 1.3 79.5 - - - +
103D MET* 1.3 68.8 + - + +
105D GLY* 3.2 10.9 + - - -
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Residues in contact with MET 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B ALA* 6.0 0.2 - - + -
126B ALA* 3.6 33.4 - - + +
127B GLN* 3.7 26.9 - - - +
302B MET 5.4 0.4 - - - +
117C ALA* 4.0 2.3 - - - +
120C LYS* 4.4 4.2 - - - +
121C GLY* 3.5 27.9 + - - -
125C HIS* 3.6 49.7 - - + +
127C TYR* 3.8 18.8 - - + +
95D ASN 4.3 1.6 - - - +
99D LYS* 3.0 19.4 + - + +
100D THR* 3.3 19.7 + - - +
102D TYR* 1.3 82.6 - - + +
104D SER* 1.3 59.3 + - - +
105D GLY 3.2 1.3 + - - -
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Residues in contact with SER 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C ALA* 3.7 13.0 - - - +
127C TYR* 3.4 31.6 - - - +
100D THR 3.1 12.1 + - - -
101D TYR 3.0 13.2 + - - -
103D MET* 1.3 75.4 - - - +
105D GLY* 1.3 59.9 + - - +
107D LEU* 3.2 23.4 + - - +
108D GLN* 3.0 34.1 + - - -
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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