Contacts of the helix formed by residues 86 - 103 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28I THR* 4.5 11.2 + - - +
29I ASP* 5.6 3.8 - - - +
67I LYS* 5.8 3.4 - - - +
83L MET* 2.8 25.2 + - - +
84L LEU 4.8 0.2 - - - -
85L ASP* 1.3 93.4 + - - +
87L PRO* 1.3 67.6 - - - +
88L ASP* 3.5 11.4 - - - +
89L MET* 3.5 28.8 + - - +
90L LEU 3.2 10.9 + - - -
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Residues in contact with PRO 87 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84L LEU 5.3 1.6 - - - +
85L ASP 3.3 12.1 - - - +
86L THR* 1.3 81.5 - - - +
88L ASP* 1.3 68.0 + - + +
90L LEU* 3.2 8.7 + - + -
91L ALA* 2.8 35.2 + - - +
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Residues in contact with ASP 88 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62I GLU 4.7 1.7 - - - +
63I SER 4.3 8.8 - - - +
64I GLY* 4.2 9.8 - - - +
65I GLU* 5.1 3.1 - - - +
67I LYS* 4.0 22.7 + - - -
86L THR* 4.0 8.7 - - - +
87L PRO* 1.3 88.2 - - + +
89L MET* 1.3 66.9 + - - +
91L ALA* 4.2 5.1 - - - +
92L ALA* 3.5 20.3 + - - +
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Residues in contact with MET 89 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28I THR* 4.5 14.8 - - + -
32I VAL* 4.6 5.8 - - + -
64I GLY* 4.3 10.8 - - - +
67I LYS* 3.4 50.7 - - + -
68I SER* 3.5 7.5 - - - +
71I VAL* 3.7 15.5 - - + -
83L MET* 3.2 35.2 - - + +
86L THR* 3.5 26.8 + - - +
87L PRO 3.2 0.4 - - - -
88L ASP* 1.3 88.6 - - - +
90L LEU* 1.3 56.7 + - - +
92L ALA* 3.3 2.4 + - - +
93L GLN* 2.7 36.6 + - - +
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Residues in contact with LEU 90 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80L THR* 4.0 28.9 - - + +
83L MET* 3.6 17.2 - - + +
84L LEU* 4.3 22.0 - - + +
86L THR 3.2 14.5 + - - +
87L PRO* 3.2 8.2 + - + +
89L MET* 1.3 76.6 - - - +
91L ALA* 1.3 59.2 + - - +
93L GLN* 3.0 4.4 + - + -
94L LEU* 2.6 74.8 + - + +
141L GLN* 3.8 26.7 - - + +
142L ILE* 4.7 3.1 - - + -
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Residues in contact with ALA 91 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87L PRO 2.8 20.9 + - - +
88L ASP* 4.2 5.8 - - - +
90L LEU* 1.3 73.7 - - - +
92L ALA* 1.3 56.7 + - - +
94L LEU* 4.0 8.1 - - - +
95L ALA* 3.1 27.5 + - - +
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Residues in contact with ALA 92 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64I GLY 4.0 16.4 - - - +
65I GLU* 4.2 23.6 - - - +
68I SER* 4.5 3.8 - - - +
88L ASP 3.5 13.9 + - - +
89L MET 3.3 8.0 + - - +
90L LEU 3.0 0.2 - - - -
91L ALA* 1.3 77.3 - - - +
93L GLN* 1.3 65.5 + - - +
95L ALA* 3.2 8.0 + - - +
96L HIS* 2.9 23.1 + - - +
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Residues in contact with GLN 93 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68I SER* 4.2 7.8 - - - -
72I ARG* 3.0 39.5 + - - +
76L GLY* 4.9 2.2 + - - -
79L ILE* 4.0 23.9 - - + +
80L THR* 4.2 15.0 - - + +
83L MET* 3.4 24.9 - - + -
89L MET 2.7 20.8 + - - +
90L LEU* 3.5 3.8 - - + +
92L ALA* 1.3 72.5 - - - +
94L LEU* 1.3 64.1 + - - +
96L HIS* 3.1 11.4 + - - +
97L LEU* 2.9 49.5 + - - +
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Residues in contact with LEU 94 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80L THR* 4.3 7.9 - - + -
90L LEU* 2.6 52.9 + - + +
91L ALA* 4.0 7.9 - - - +
93L GLN* 1.3 73.7 - - - +
95L ALA* 1.3 64.6 + - - +
97L LEU* 2.9 16.5 + - - +
98L LYS 2.9 11.1 + - - -
141L GLN* 4.0 19.5 - - + +
142L ILE* 3.3 43.3 - - + +
145L GLY* 3.5 21.9 - - - +
146L ILE* 4.3 6.7 - - + +
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Residues in contact with ALA 95 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91L ALA 3.1 16.9 + - - +
92L ALA* 3.4 7.4 - - - +
94L LEU* 1.3 78.8 - - - +
96L HIS* 1.3 62.7 + - - +
98L LYS* 3.3 17.2 + - - +
99L VAL* 3.3 19.4 + - - +
145L GLY 4.6 1.8 - - - -
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Residues in contact with HIS 96 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55I ARG* 4.0 25.9 + - - -
72I ARG* 3.5 44.4 + - + +
160I HEM 3.1 35.3 + - - -
92L ALA 2.9 13.2 + - - +
93L GLN* 3.2 17.5 - - - +
95L ALA* 1.3 79.4 - - - +
97L LEU* 1.3 60.3 + - - +
99L VAL* 3.5 14.3 + - - +
100L GLN* 3.3 36.3 + - + +
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Residues in contact with LEU 97 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76L GLY* 4.9 4.0 - - - +
80L THR* 3.6 32.1 - - + -
93L GLN* 2.9 30.0 + - + +
94L LEU* 2.9 9.4 + - - +
96L HIS* 1.3 74.2 - - - +
98L LYS* 1.3 68.1 + - - +
100L GLN* 3.1 25.5 + - - +
101L HIS* 3.1 20.5 + - + +
146L ILE* 3.6 30.3 - - + -
160L HEM 3.9 43.7 - - + -
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Residues in contact with LYS 98 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94L LEU 2.9 5.8 + - - +
95L ALA* 3.3 12.5 + - - +
97L LEU* 1.3 75.6 - - - +
99L VAL* 1.3 59.0 + - + +
101L HIS* 3.1 2.6 + - - +
102L VAL* 2.8 38.6 + - + +
144L ASP 5.0 5.5 + - - -
145L GLY* 3.5 23.3 - - - +
146L ILE* 3.7 22.7 - - - +
147L LYS 3.5 18.9 + - - +
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Residues in contact with VAL 99 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95L ALA 3.3 16.4 - - - +
96L HIS* 3.6 10.8 - - - +
97L LEU 3.1 0.6 - - - -
98L LYS* 1.3 73.4 - - + +
100L GLN* 1.3 61.3 + - + +
101L HIS 2.8 11.0 + - - -
102L VAL* 3.3 25.1 + - + +
103L GLU* 3.6 16.9 - - + +
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Residues in contact with GLN 100 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100I GLN* 5.2 0.5 + - - -
160I HEM 3.9 16.5 + - - +
96L HIS* 3.3 49.0 + - + +
97L LEU* 3.1 25.0 + - - +
99L VAL* 1.3 75.8 - - + +
101L HIS* 1.3 67.1 + - + +
103L GLU* 5.0 3.2 - - - +
104L ARG* 3.0 32.7 + - - +
160L HEM 3.4 37.5 - - + +
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Residues in contact with HIS 101 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97L LEU* 3.1 21.9 + - + +
98L LYS 3.1 6.9 + - - +
99L VAL 2.8 2.8 + - - -
100L GLN* 1.3 84.7 - - + +
102L VAL* 1.3 67.1 + - - +
103L GLU* 2.7 6.0 + - - -
104L ARG* 2.9 16.1 + - - +
106L LEU* 3.3 23.6 - - + +
111L PHE* 3.6 20.9 - + + -
146L ILE* 4.1 15.5 - - + +
160L HEM 2.0 93.1 + + + -
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Residues in contact with VAL 102 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98L LYS* 2.8 29.7 + - + +
99L VAL* 3.3 24.0 - - + +
101L HIS* 1.3 70.8 - - - +
103L GLU* 1.3 67.2 + - + +
104L ARG 2.7 20.5 + - - +
106L LEU* 5.1 1.6 - - - -
146L ILE 5.6 0.6 + - - -
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Residues in contact with GLU 103 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99L VAL* 3.6 23.7 - - + +
100L GLN* 5.1 3.6 - - - +
101L HIS 2.7 6.1 + - - +
102L VAL* 1.3 80.0 - - + +
104L ARG* 1.3 68.0 + - + +
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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