Contacts of the helix formed by residues 63 - 82 (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 SER 63 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57L ARG* 3.8 25.7 - - - +
60L ASN* 2.6 38.0 + - - +
61L ILE 3.9 0.2 - - - +
62L TYR* 1.3 79.1 - - - +
64L PRO* 1.3 70.5 - - - +
65L GLU 3.7 2.0 + - - -
66L PHE* 3.1 17.3 + - - +
67L GLY* 2.8 25.5 + - - -
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Residues in contact with PRO 64 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88I LEU* 3.8 43.5 - - + +
89I VAL* 3.9 15.6 - - + +
92I SER* 4.7 3.8 - - - -
62L TYR 3.8 1.5 - - - +
63L SER* 1.3 85.3 - - - +
65L GLU* 1.3 89.6 + - - +
68L ALA* 2.7 26.5 + - - +
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Residues in contact with GLU 65 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92I SER* 4.0 21.0 + - - +
55L ARG 5.8 2.0 - - - +
56L VAL* 4.3 13.2 - - - +
57L ARG* 3.2 44.0 + - + -
63L SER* 3.3 0.9 - - - +
64L PRO* 1.3 103.8 - - - +
66L PHE* 1.3 62.0 + - - +
68L ALA* 3.4 4.9 - - - +
69L HIS* 3.3 16.1 + - - +
72L ARG* 4.7 0.9 + - - -
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Residues in contact with PHE 66 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36L LEU* 5.4 3.4 - - + -
39L TRP* 3.7 41.7 - + + -
43L ILE* 4.6 4.5 - - + -
53L PHE* 4.1 18.4 - + - -
56L VAL* 3.2 19.4 + - + -
57L ARG 3.4 18.6 - - - +
58L GLY* 4.0 9.0 - - - -
60L ASN 3.8 3.1 - - - +
61L ILE* 3.2 47.3 - - + +
63L SER* 3.1 10.8 + - - +
65L GLU* 1.3 76.2 - - - +
67L GLY* 1.3 68.6 + - - +
69L HIS* 2.9 28.6 + + - +
70L SER* 2.7 27.8 + - - -
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Residues in contact with GLY 67 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89I VAL* 4.0 14.2 - - - +
32L VAL* 5.4 8.4 - - - +
61L ILE 4.6 5.2 - - - -
62L TYR 5.8 0.2 - - - -
63L SER 2.8 17.9 + - - -
64L PRO 3.5 2.0 - - - -
66L PHE* 1.3 78.5 - - - +
68L ALA* 1.3 64.0 + - - +
70L SER* 3.3 9.6 - - - -
71L GLN* 3.1 23.0 + - - +
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Residues in contact with ALA 68 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79I LEU* 5.7 0.3 - - - +
83I LEU* 5.6 0.2 - - - -
89I VAL* 3.5 16.6 - - + +
92I SER* 4.2 5.6 - - - +
93I HIS* 3.9 24.6 - - + +
64L PRO 2.7 15.8 + - - +
65L GLU 3.4 11.0 - - - +
67L GLY* 1.3 69.4 - - - +
69L HIS* 1.3 66.8 + - - +
71L GLN* 2.9 16.4 + - - +
72L ARG* 3.0 31.8 + - - +
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Residues in contact with HIS 69 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39L TRP* 4.9 1.5 - - - -
53L PHE* 3.3 12.9 - + - -
56L VAL* 3.8 22.4 - - + -
65L GLU 3.3 1.6 + - - +
66L PHE* 2.9 33.3 + + - +
68L ALA* 1.3 78.2 - - - +
70L SER* 1.3 67.3 + - - +
72L ARG* 2.7 45.8 + - - +
73L VAL* 2.9 24.4 + - + +
160L HEM 3.7 39.4 + + + +
161L CMO 2.9 29.0 + - - -
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Residues in contact with SER 70 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32L VAL* 4.8 1.5 + - - +
35L GLY* 3.4 31.7 - - - -
36L LEU* 3.9 3.0 + - - -
39L TRP* 3.7 23.0 - - - +
66L PHE* 2.7 20.9 + - - -
67L GLY* 3.3 15.0 - - - -
69L HIS* 1.3 75.4 - - - +
71L GLN* 1.3 66.5 + - - +
73L VAL* 3.3 3.3 - - - +
74L LEU* 2.9 28.8 + - - +
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Residues in contact with GLN 71 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79I LEU* 3.4 29.9 - - + +
82I ASN 5.7 0.4 + - - +
83I LEU* 3.7 21.5 - - + -
89I VAL* 5.5 0.8 - - + +
25L PHE* 4.3 9.9 - - - -
28L ALA 5.0 0.2 + - - -
31L ARG* 3.2 41.5 + - - +
32L VAL* 3.4 30.4 - - - +
35L GLY* 5.3 0.6 - - - -
67L GLY 3.1 9.9 + - - +
68L ALA* 2.9 11.3 + - - +
70L SER* 1.3 83.2 + - - +
72L ARG* 1.3 67.4 + - - +
73L VAL 3.0 0.3 + - - -
74L LEU* 3.1 5.8 + - - +
75L SER* 2.8 24.9 + - - -
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Residues in contact with ARG 72 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79I LEU* 4.9 5.4 - - + -
92I SER* 5.5 0.4 + - - -
93I HIS* 3.4 32.3 + - + +
96I HIS* 3.3 54.5 + - - +
100I GLN* 5.8 0.2 - - - -
55L ARG* 4.4 1.4 - - - +
56L VAL* 3.7 17.2 - - - +
65L GLU 4.7 1.2 + - - -
68L ALA* 3.0 32.4 + - - +
69L HIS* 2.7 40.5 + - - +
71L GLN* 1.3 72.3 - - - +
73L VAL* 1.3 63.8 + - + +
75L SER* 3.3 8.2 - - - -
76L GLY 3.1 14.7 + - - -
160L HEM 4.0 35.5 + - + +
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Residues in contact with VAL 73 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39L TRP* 4.0 15.7 - - + +
69L HIS* 2.9 33.0 + - + +
70L SER* 3.3 8.3 - - - +
72L ARG* 1.3 72.0 - - - +
74L LEU* 1.3 76.8 + - + +
76L GLY* 2.7 15.6 + - - -
77L LEU* 3.0 9.1 + - + +
114L PHE* 4.6 7.6 - - + -
160L HEM 3.9 30.6 - - + +
161L CMO 3.2 37.5 - - - +
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Residues in contact with LEU 74 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21L TRP* 3.8 20.4 - - + -
25L PHE* 3.6 24.9 - - + -
34L PHE* 3.8 30.3 - - + -
35L GLY* 4.1 21.3 - - - -
38L LEU* 4.5 10.5 - - + -
39L TRP* 4.2 9.2 - - - +
70L SER* 2.9 26.9 - - - +
71L GLN* 3.1 10.9 + - - +
73L VAL* 1.3 86.4 - - + +
75L SER* 1.3 64.1 + - - +
77L LEU* 3.0 18.5 + - + +
78L ASP* 2.8 21.0 + - - +
114L PHE* 5.8 0.7 - - + -
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Residues in contact with SER 75 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75I ASN* 3.4 32.4 + - - +
78I LYS* 5.8 0.9 - - - +
79I LEU* 4.2 18.2 - - - +
25L PHE* 4.7 4.9 - - - -
31L ARG* 6.3 1.1 - - - +
71L GLN 2.8 17.1 + - - -
72L ARG* 3.3 11.7 - - - -
74L LEU* 1.3 72.9 - - - +
76L GLY* 1.3 59.2 + - - +
78L ASP* 2.8 26.4 + - - +
79L ILE* 2.9 14.7 + - - +
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Residues in contact with GLY 76 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72L ARG 3.1 6.2 + - - -
73L VAL 2.7 14.3 + - - -
75L SER* 1.3 75.4 - - - +
77L LEU* 1.3 60.1 + - - -
79L ILE* 3.0 18.6 + - - +
80L THR* 2.9 29.5 + - - +
93L GLN* 4.9 5.0 + - - -
97L LEU* 5.3 2.0 - - - -
160L HEM 4.4 17.7 - - - -
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Residues in contact with LEU 77 (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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21L TRP* 3.9 22.2 - - + -
73L VAL* 3.0 7.3 + - + +
74L LEU* 3.0 21.5 + - + +
76L GLY* 1.3 76.2 - - - +
78L ASP* 1.3 60.8 + - - +
80L THR* 2.6 28.5 + - - +
81L ILE* 3.0 31.9 + - + +
114L PHE* 4.4 12.1 - - + -
118L LEU* 3.5 36.6 - - + -
139L VAL* 5.0 5.4 - - + -
142L ILE* 4.8 8.5 - - + -
160L HEM 4.0 28.2 - - + +
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Residues in contact with ASP 78 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I TRP* 5.3 1.9 + - - -
31I ARG* 4.0 11.1 + - - -
75I ASN* 3.8 15.1 + - - +
78I LYS* 5.0 4.2 + - - -
21L TRP* 3.3 33.4 + - + +
25L PHE* 4.0 15.9 - - + -
31L ARG* 4.4 7.1 + - - -
74L LEU 2.8 12.1 + - - +
75L SER* 2.8 17.6 + - - +
77L LEU* 1.3 77.6 - - - +
79L ILE* 1.3 61.7 + - - +
81L ILE* 3.2 2.8 + - - +
82L SER* 2.8 28.4 + - - -
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Residues in contact with ILE 79 (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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71I VAL* 3.6 21.3 - - + -
72I ARG* 4.0 26.2 - - + -
75I ASN* 3.4 39.9 - - + +
75L SER* 2.9 7.0 + - - +
76L GLY* 3.2 18.6 - - - +
78L ASP* 1.3 75.7 - - - +
80L THR* 1.3 67.7 + - - +
82L SER* 2.5 26.3 + - - -
83L MET* 3.1 26.4 + - + +
93L GLN* 4.0 17.0 - - - +
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Residues in contact with THR 80 (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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76L GLY 2.9 12.8 + - - +
77L LEU* 2.6 27.6 + - - +
79L ILE* 1.3 74.8 - - - +
81L ILE* 1.3 55.3 + - - +
83L MET* 2.7 30.3 + - - +
84L LEU* 2.9 14.9 - - - +
90L LEU* 4.0 9.4 - - - +
93L GLN* 4.2 9.6 - - + -
94L LEU* 4.3 4.0 - - + -
97L LEU* 3.6 29.2 - - + -
142L ILE* 3.4 35.7 - - + +
160L HEM 5.0 0.9 - - + -
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Residues in contact with ILE 81 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17L VAL* 4.1 13.5 - - + -
18L LYS* 3.1 29.1 + - - +
21L TRP* 3.8 37.9 - - + -
77L LEU* 3.0 33.4 + - + +
78L ASP* 3.5 4.0 - - - +
80L THR* 1.3 85.1 + - - +
82L SER* 1.3 58.3 + - - +
83L MET 3.0 4.7 + - - -
84L LEU* 3.3 30.4 + - + +
135L TRP* 4.0 20.2 - - + -
139L VAL* 5.1 2.0 - - + -
142L ILE* 4.1 11.0 - - + -
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Residues in contact with SER 82 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I SER* 3.7 17.9 - - - -
28I THR* 3.4 27.8 + - - +
31I ARG* 3.8 22.1 + - - -
71I VAL* 5.1 0.2 - - - +
18L LYS* 3.2 19.5 + - - +
78L ASP* 2.8 17.0 + - - -
79L ILE* 2.5 31.3 + - - +
81L ILE* 1.3 72.5 - - - +
83L MET* 1.3 57.9 + - - +
85L ASP* 3.4 5.9 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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