Contacts of the helix formed by residues 97 - 110 (chain D) in PDB entry 3GXM
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 SER 97 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A THR* 5.0 9.4 - - - -
189A GLY 5.0 6.1 - - - -
20D ALA* 3.6 17.2 - - - +
95D ALA 3.8 0.6 + - - -
96D LEU* 1.3 72.5 - - - +
98D PRO* 1.3 76.3 - - - +
99D PRO* 3.6 6.9 - - - +
100D ALA* 3.0 14.4 + - - +
101D GLN* 3.1 10.2 + - - +
409D ASP* 2.4 38.3 + - - -
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Residues in contact with PRO 98 (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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137A ASP* 5.0 16.2 - - + +
139A PRO* 5.6 10.5 - - + -
183A THR* 6.0 0.9 - - - +
96D LEU 4.3 0.2 - - - +
97D SER* 1.3 85.8 - - - +
99D PRO* 1.4 66.6 - - + +
101D GLN* 3.7 23.1 + - - +
102D ASN* 2.9 33.0 + - - +
163D ARG* 4.3 2.0 + - - +
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Residues in contact with PRO 99 (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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20D ALA* 3.2 28.0 - - + +
97D SER* 3.4 14.1 - - - +
98D PRO* 1.4 93.7 - - + +
100D ALA* 1.3 59.3 + - - +
102D ASN* 3.5 9.8 + - + +
103D LEU* 3.0 31.7 + - - +
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Residues in contact with ALA 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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19D ASN* 3.9 9.6 - - - -
20D ALA* 3.8 22.0 - - - +
96D LEU* 3.9 13.9 - - + -
97D SER* 3.0 20.1 + - - +
99D PRO* 1.3 79.5 - - - +
101D GLN* 1.3 57.6 + - - +
103D LEU* 3.0 3.5 + - - +
104D LEU* 2.8 25.8 + - - +
409D ASP* 3.9 15.5 - - - +
411D PHE* 3.5 11.0 - - + -
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Residues in contact with GLN 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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93D ILE* 2.8 36.7 - - + +
94D LEU* 3.6 24.7 + - - +
96D LEU* 2.6 27.1 + - + +
97D SER 3.1 10.2 + - - +
98D PRO* 3.7 26.2 - - - +
99D PRO 3.4 0.2 - - - -
100D ALA* 1.3 74.6 - - - +
102D ASN* 1.3 52.6 - - - +
104D LEU* 3.2 6.3 + - - +
105D LEU* 2.8 37.8 + - - +
163D ARG* 3.0 35.8 + - - +
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Residues in contact with ASN 102 (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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98D PRO* 2.9 21.6 + - - +
99D PRO* 3.7 10.1 - - + +
101D GLN* 1.3 71.0 - - - +
103D LEU* 1.3 64.7 + - + +
105D LEU* 3.4 6.8 + - - +
106D LYS* 2.9 48.1 + - - +
163D ARG* 2.8 29.8 + - - +
167D LEU* 4.7 6.9 - - + +
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Residues in contact with LEU 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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19D ASN 3.0 24.7 - - - +
20D ALA 3.8 15.3 - - - +
21D THR 4.2 2.7 - - - -
22D TYR 3.9 23.6 - - - +
23D CYS* 3.8 19.7 - - + +
99D PRO 3.0 14.4 + - - +
100D ALA 3.0 8.2 + - - +
102D ASN* 1.3 76.3 - - + +
104D LEU* 1.3 51.7 + - - +
106D LYS* 3.4 19.0 + - + +
107D SER* 2.8 34.7 + - - -
411D PHE* 3.8 6.3 - - + -
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Residues in contact with LEU 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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93D ILE* 4.1 33.0 - - + -
96D LEU* 3.6 25.6 - - + -
100D ALA 2.8 12.1 + - - +
101D GLN* 3.3 10.1 - - - +
103D LEU* 1.3 73.8 - - - +
105D LEU* 1.3 71.3 + - + +
107D SER* 3.3 18.3 + - - -
108D TYR* 3.6 20.3 + - + -
383D LEU* 6.0 0.9 - - + -
384D ALA* 4.9 3.1 - - + -
402D ILE* 4.0 30.7 - - + +
404D VAL* 4.2 6.7 - - + -
411D PHE* 3.4 24.3 - - + -
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Residues in contact with LEU 105 (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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85D MET* 5.0 8.5 - - + -
93D ILE* 3.6 19.1 - - + -
101D GLN 2.8 23.5 + - - +
102D ASN* 3.4 3.1 + - - +
104D LEU* 1.3 79.5 - - + +
106D LYS* 1.3 55.9 + - - +
108D TYR 3.4 0.2 + - - -
109D PHE* 2.9 57.3 + - + +
160D LEU* 4.0 26.0 - - + +
163D ARG* 3.8 39.3 - - + +
164D ALA* 4.4 4.0 - - + +
167D LEU* 3.3 21.3 - - + +
383D LEU* 6.2 0.4 - - + -
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Residues in contact with LYS 106 (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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102D ASN* 2.9 32.7 + - - +
103D LEU* 3.6 20.6 - - + +
105D LEU* 1.3 74.1 - - - +
107D SER* 1.3 67.4 + - - +
108D TYR 3.1 0.7 + - - -
110D SER* 3.1 35.2 + - - +
112D GLU* 4.4 27.1 - - + +
113D GLY* 3.5 9.3 + - - -
167D LEU* 3.4 28.7 - - + +
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Residues in contact with SER 107 (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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23D CYS* 3.8 9.0 - - - -
24D ASP 5.0 1.3 + - - -
103D LEU 2.8 19.5 + - - -
104D LEU* 3.3 12.4 + - - -
106D LYS* 1.3 76.3 - - - +
108D TYR* 1.3 56.7 + - - +
113D GLY* 3.3 6.4 - - - -
114D ILE* 2.9 22.3 + - - +
402D ILE* 4.4 5.6 - - - -
411D PHE* 4.1 1.6 - - - -
413D LYS* 3.4 28.2 + - - +
417D PHE* 3.1 28.3 - - - -
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Residues in contact with TYR 108 (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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104D LEU* 3.6 20.1 + - + -
105D LEU* 3.4 1.7 + - + +
106D LYS 3.1 0.2 - - - -
107D SER* 1.3 81.5 - - - +
109D PHE* 1.3 77.5 + + + +
110D SER 3.7 0.7 - - - -
114D ILE* 3.7 4.0 - - + -
115D GLY 3.3 6.1 + - - -
116D TYR* 2.6 76.0 + + + +
380D ASP* 5.0 0.7 + - - -
383D LEU* 2.5 54.4 + - + -
401D PRO* 3.9 10.8 - - + +
402D ILE* 3.6 29.6 + - + +
417D PHE* 3.7 24.5 - + - -
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Residues in contact with PHE 109 (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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85D MET* 5.3 0.7 - - + -
105D LEU* 2.9 39.1 + - + +
108D TYR* 1.3 103.1 - + + +
110D SER* 1.3 63.4 + - - +
115D GLY* 4.2 7.6 - - - -
116D TYR* 3.6 39.6 - + + +
118D ILE 4.4 1.1 - - - -
119D ILE* 3.6 38.1 - - + -
164D ALA* 3.5 41.3 - - + +
167D LEU* 4.3 3.8 - - + -
168D ALA* 3.4 22.0 - - + +
169D GLN* 4.7 0.5 + - - -
172D VAL* 5.1 6.3 - - + -
383D LEU* 4.1 19.7 - - + -
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Residues in contact with SER 110 (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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105D LEU 4.1 0.4 + - - -
106D LYS* 3.1 33.2 + - - +
109D PHE* 1.3 79.3 - - - +
111D GLU* 1.3 58.7 + - - +
112D GLU* 2.8 35.5 + - - +
113D GLY 3.1 14.3 + - - -
115D GLY* 3.3 19.9 + - - -
167D LEU* 3.7 20.4 - - - -
169D GLN* 4.4 1.3 - - - -
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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