Contacts of the helix formed by residues 86 - 103 (chain D) in PDB entry 2GTL
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 THR 86 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A THR* 4.0 13.7 + - - +
29A ASP* 5.1 6.7 - - - +
67A LYS* 5.9 3.6 - - - +
83D MET* 2.8 25.6 + - - +
84D LEU 4.8 0.2 - - - -
85D ASP* 1.3 92.0 - - - +
87D PRO* 1.3 68.7 - - - +
88D ASP* 3.5 11.9 - - - +
89D MET* 3.5 26.3 + - - +
90D LEU 3.2 10.6 + - - -
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Residues in contact with PRO 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D LEU 4.9 2.2 - - - +
85D ASP 3.3 11.6 - - - +
86D THR* 1.3 81.1 - - - +
88D ASP* 1.3 66.9 + - + +
90D LEU* 3.7 8.2 - - + +
91D ALA* 2.8 35.5 + - - +
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Residues in contact with ASP 88 (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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62A GLU 4.6 1.4 - - - +
63A SER 4.4 9.5 - - - +
64A GLY* 4.1 10.0 - - - +
65A GLU* 5.3 1.9 - - - +
67A LYS* 3.5 31.2 + - - -
86D THR* 4.0 9.4 - - - +
87D PRO* 1.3 87.7 - - + +
89D MET* 1.3 64.4 + - - +
91D ALA* 4.2 4.9 - - - +
92D ALA* 3.4 21.0 + - - +
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Residues in contact with MET 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A THR* 4.2 13.2 - - + -
32A VAL* 4.2 7.9 - - + -
64A GLY 4.3 8.3 - - - +
67A LYS* 3.5 46.0 - - + +
68A SER* 3.9 1.8 - - - +
71A VAL* 3.3 34.5 - - + -
83D MET* 3.2 27.4 - - + +
86D THR* 3.5 26.9 + - - +
87D PRO 3.2 0.6 - - - -
88D ASP* 1.3 87.7 - - - +
90D LEU* 1.3 56.1 + - - +
92D ALA* 3.3 2.1 + - - +
93D GLN* 2.7 36.9 + - - +
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Residues in contact with LEU 90 (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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80D THR* 3.9 28.5 - - + +
83D MET* 3.6 17.2 - - + +
84D LEU* 4.2 22.2 - - + +
86D THR 3.2 14.5 + - - +
87D PRO* 3.2 9.3 + - + +
89D MET* 1.3 75.8 - - - +
91D ALA* 1.3 59.5 - - - +
93D GLN* 3.0 3.7 + - + -
94D LEU* 2.6 73.8 + - + +
141D GLN* 3.7 26.9 - - + +
142D ILE* 4.7 3.1 - - + -
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Residues in contact with ALA 91 (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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87D PRO 2.8 21.1 + - - +
88D ASP* 4.2 5.4 - - - +
90D LEU* 1.3 74.2 - - - +
92D ALA* 1.3 60.9 + - - +
94D LEU* 3.9 8.5 - - - +
95D ALA* 3.2 23.4 + - - +
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Residues in contact with ALA 92 (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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64A GLY 3.8 17.3 - - - +
65A GLU* 4.2 21.1 - - + +
68A SER* 4.2 5.4 - - - +
88D ASP 3.4 13.4 + - - +
89D MET 3.3 7.8 + - - +
90D LEU 3.0 0.6 - - - -
91D ALA* 1.3 77.7 - - - +
93D GLN* 1.3 65.6 + - - +
95D ALA* 3.2 6.9 + - - +
96D HIS* 2.9 23.1 + - - +
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Residues in contact with GLN 93 (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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68A SER* 4.3 6.9 - - - +
72A ARG* 2.8 39.6 + - - +
76D GLY* 4.9 1.4 + - - -
79D ILE* 4.0 24.3 - - + +
80D THR* 4.2 14.8 - - + +
83D MET* 3.5 24.6 - - + +
89D MET 2.7 20.9 + - - +
90D LEU* 3.6 2.9 - - + +
92D ALA* 1.3 72.7 - - - +
94D LEU* 1.3 65.2 + - - +
96D HIS* 3.0 11.1 + - - +
97D LEU* 2.9 49.5 + - - +
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Residues in contact with LEU 94 (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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80D THR* 4.3 8.3 - - + -
90D LEU* 2.6 53.3 + - + +
91D ALA* 3.9 7.0 - - - +
93D GLN* 1.3 73.6 - - - +
95D ALA* 1.3 64.5 + - - +
97D LEU* 2.9 16.0 + - - +
98D LYS 2.9 11.1 + - - -
141D GLN* 3.9 20.2 - - + +
142D ILE* 3.3 42.0 - - + +
145D GLY* 3.5 22.8 - - - +
146D ILE* 4.3 6.2 - - + +
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Residues in contact with ALA 95 (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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91D ALA 3.2 17.7 + - - +
92D ALA* 3.4 7.6 - - - +
94D LEU* 1.3 78.4 - - - +
96D HIS* 1.3 62.8 + - - +
98D LYS* 3.3 18.4 + - - +
99D VAL* 3.4 18.9 + - - +
145D GLY 4.4 2.0 + - - -
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Residues in contact with HIS 96 (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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55A ARG* 4.2 20.5 + - - -
72A ARG* 3.5 46.3 + - + +
104A ARG* 6.0 0.2 - - - -
160A HEM 2.9 36.4 + - - -
92D ALA 2.9 12.6 + - - +
93D GLN* 3.2 18.2 - - - +
95D ALA* 1.3 78.9 - - - +
97D LEU* 1.3 61.2 + - - +
99D VAL* 3.5 14.5 + - - +
100D GLN* 3.4 37.0 + - + +
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Residues in contact with LEU 97 (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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76D GLY* 4.9 4.0 - - - +
80D THR* 3.6 29.6 - - + -
93D GLN* 2.9 30.4 + - - +
94D LEU* 2.9 10.1 + - - +
96D HIS* 1.3 74.5 - - - +
98D LYS* 1.3 66.9 + - - +
100D GLN* 3.1 29.6 + - - +
101D HIS* 3.2 19.4 + - + +
146D ILE* 3.5 32.3 - - + -
160D HEM 4.0 40.2 - - + -
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Residues in contact with LYS 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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94D LEU 2.9 5.6 + - - +
95D ALA* 3.3 12.3 + - - +
97D LEU* 1.3 75.7 - - - +
99D VAL* 1.3 58.8 + - + +
101D HIS* 3.1 2.3 + - - +
102D VAL* 2.8 40.1 + - + +
144D ASP 5.0 5.3 + - - -
145D GLY* 3.5 24.0 - - - +
146D ILE* 3.6 22.4 - - - +
147D LYS 3.5 18.2 + - - +
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Residues in contact with VAL 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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95D ALA 3.4 15.9 - - - +
96D HIS* 3.6 10.8 - - - +
97D LEU 3.1 0.6 - - - -
98D LYS* 1.3 73.6 - - + +
100D GLN* 1.3 60.7 + - + +
101D HIS 2.8 10.5 + - - -
102D VAL* 3.2 23.6 - - + +
103D GLU* 3.6 17.2 - - + +
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Residues in contact with GLN 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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100A GLN* 5.1 1.2 + - - -
160A HEM 3.9 15.4 + - - +
96D HIS* 3.4 48.4 + - + +
97D LEU* 3.1 25.4 + - - +
99D VAL* 1.3 77.1 - - + +
101D HIS* 1.3 67.3 + - + +
103D GLU* 5.0 2.9 - - - +
104D ARG* 3.0 31.3 + - - +
160D HEM 3.4 36.5 - - + +
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Residues in contact with HIS 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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97D LEU* 3.2 21.3 + - + +
98D LYS* 3.1 6.7 + - - +
99D VAL 2.8 2.4 + - - -
100D GLN* 1.3 84.2 - - + +
102D VAL* 1.3 67.5 + - - +
103D GLU* 2.7 5.1 + - - -
104D ARG* 2.9 16.9 + - - +
106D LEU* 3.2 23.8 - - + +
111D PHE* 3.7 21.3 - + + -
146D ILE* 4.1 15.5 - - + +
160D HEM 2.0 93.7 + + + -
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Residues in contact with VAL 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 LYS* 2.8 27.5 + - + +
99D VAL* 3.2 23.3 - - + +
101D HIS* 1.3 71.3 - - - +
103D GLU* 1.3 66.8 + - + +
104D ARG 2.7 20.6 + - - +
106D LEU* 5.1 1.6 - - - -
146D ILE 5.5 1.0 + - - -
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Residues in contact with GLU 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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99D VAL* 3.6 23.5 - - + +
100D GLN* 5.2 4.3 - - - +
101D HIS 2.7 6.3 + - - +
102D VAL* 1.3 79.2 - - + +
104D ARG* 1.3 68.1 + - + +
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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