Contacts of the helix formed by residues 81 - 97 (chain F) 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 GLN 81 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29E ASP* 6.2 0.2 - - - +
77F SER 4.2 2.2 + - - -
78F THR* 2.9 16.2 + - - +
80F ASP* 1.3 102.1 + - - +
82F PRO* 1.3 70.8 - - - +
83F ALA* 2.8 6.0 + - + -
84F THR* 2.9 30.5 + - - +
85F LEU 3.0 8.8 + - - -
29G SER* 3.0 35.2 + - - -
30G LYS* 3.5 28.4 + - - +
33G ILE* 4.1 11.9 - - - +
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Residues in contact with PRO 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F THR 4.2 0.2 - - - -
79F LEU 4.9 3.8 - - - +
80F ASP* 3.7 6.5 - - - +
81F GLN* 1.3 87.8 - - - +
83F ALA* 1.3 68.4 + - + +
85F LEU* 4.4 11.4 - - + +
86F LYS* 2.9 27.4 + - - +
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Residues in contact with ALA 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81F GLN* 2.8 6.7 + - + +
82F PRO* 1.3 83.2 - - + +
84F THR* 1.3 64.6 + - - +
86F LYS* 3.2 15.0 - - - +
87F GLU* 3.5 4.9 + - - +
65G PRO* 3.6 27.5 - - + +
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Residues in contact with THR 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F THR* 4.6 6.3 - - + -
81F GLN* 2.9 30.8 + - - +
83F ALA* 1.3 71.9 - - - +
85F LEU* 1.3 69.3 + - - +
87F GLU* 2.6 21.7 + - - +
88F GLU* 3.1 5.9 + - + +
33G ILE* 4.6 8.3 - - + -
65G PRO* 3.8 11.9 - - - +
68G SER* 4.0 18.3 - - - +
69G ALA* 3.7 33.0 - - + +
72G LEU* 4.6 8.5 - - + -
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Residues in contact with LEU 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75F ALA* 3.5 32.1 - - + +
78F THR* 3.4 29.4 + - - +
79F LEU* 3.9 27.4 - - + +
81F GLN 3.0 6.8 + - - +
82F PRO* 3.9 9.2 - - + +
84F THR* 1.3 77.3 - - - +
86F LYS* 1.3 67.8 + - - +
88F GLU* 2.9 7.7 + - + +
89F LEU* 2.8 59.7 + - + +
136F HIS* 4.2 18.2 - - + +
137F ILE* 5.1 0.7 - - + -
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Residues in contact with LYS 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82F PRO 2.9 21.4 + - - +
83F ALA* 3.2 9.4 - - - +
85F LEU* 1.3 78.2 - - - +
87F GLU* 1.3 66.4 + - - +
89F LEU* 3.3 7.5 + - - +
90F ASP* 2.8 61.8 + - - +
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Residues in contact with GLU 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83F ALA 3.5 9.0 + - - +
84F THR 2.6 17.9 + - - +
86F LYS* 1.3 83.7 - - - +
88F GLU* 1.3 63.9 + - - +
90F ASP* 3.0 14.1 + - - +
91F HIS* 2.8 23.0 + - - +
65G PRO* 4.1 8.6 - - - +
66G LYS* 3.2 63.4 + - + +
69G ALA* 3.7 15.3 - - + -
73G ARG* 5.2 2.2 - - - +
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Residues in contact with GLU 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F GLY* 4.3 4.8 - - - +
74F ILE* 3.6 44.6 - - + +
75F ALA* 4.3 10.3 - - + +
84F THR* 3.1 5.8 + - + +
85F LEU* 2.9 15.4 + - + +
87F GLU* 1.3 74.2 - - - +
89F LEU* 1.3 65.7 + - - +
91F HIS* 3.0 9.2 + - - +
92F LEU* 2.9 54.4 + - + +
95F GLN* 5.4 0.3 + - - -
69G ALA* 4.1 9.1 - - + +
73G ARG* 2.9 34.9 + - - +
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Residues in contact with LEU 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75F ALA* 4.4 5.4 - - + -
85F LEU* 2.8 52.4 + - + +
86F LYS* 3.6 8.7 - - - +
88F GLU* 1.3 72.0 - - - +
90F ASP* 1.3 53.4 + - - +
92F LEU* 3.0 11.0 + - + +
93F GLN* 2.7 33.8 + - - +
136F HIS* 4.5 13.7 - - + +
137F ILE* 3.3 44.4 - - + +
140F GLY* 3.6 26.6 - - - +
141F ILE* 4.1 8.1 - - + -
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Residues in contact with ASP 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86F LYS* 2.8 48.8 + - - +
87F GLU* 3.3 18.2 - - - +
89F LEU* 1.3 77.8 - - - +
91F HIS* 1.3 64.1 + - - +
93F GLN* 3.1 38.0 + - - +
94F VAL* 3.2 13.0 + - - +
140F GLY 4.9 1.4 - - - +
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Residues in contact with HIS 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87F GLU 2.8 16.0 + - - +
88F GLU* 3.2 12.5 + - - +
90F ASP* 1.3 73.5 - - - +
92F LEU* 1.3 66.2 + - - +
94F VAL* 3.1 14.9 + - + +
95F GLN* 3.3 25.0 + - + +
56G ARG* 5.2 17.0 + - - +
73G ARG* 2.8 56.5 + - + +
160G HEM 3.2 44.0 + - + -
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Residues in contact with LEU 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F GLY* 4.9 8.5 - - - +
75F ALA* 5.3 2.7 - - + -
88F GLU* 2.9 41.2 + - + +
89F LEU* 3.3 14.6 - - + +
91F HIS* 1.3 71.5 - - - +
93F GLN* 1.3 68.9 + - - +
95F GLN* 2.7 37.7 + - - +
96F HIS* 3.1 18.8 + - + +
141F ILE* 3.6 35.2 - - + -
160F HEM 3.9 39.5 - - + -
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Residues in contact with GLN 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89F LEU 2.7 15.4 + - - +
90F ASP* 3.1 28.0 + - - +
92F LEU* 1.3 72.3 - - - +
94F VAL* 1.3 60.1 + - - +
96F HIS* 3.3 2.3 + - - +
97F GLU* 2.9 36.9 + - + +
140F GLY* 3.6 16.9 + - - +
141F ILE* 3.4 27.5 - - - +
142F LYS 4.6 5.4 - - - +
143F GLY* 4.0 20.4 - - - -
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Residues in contact with VAL 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90F ASP 3.4 14.8 - - - +
91F HIS* 3.1 11.9 + - + +
92F LEU 2.8 3.8 + - - -
93F GLN* 1.3 74.2 - - + +
95F GLN* 1.3 61.7 + - + +
96F HIS 2.7 11.1 + - - -
97F GLU* 3.3 38.7 + - - +
56G ARG* 6.0 5.4 - - - +
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Residues in contact with GLN 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88F GLU* 5.4 0.2 + - - -
91F HIS* 3.4 38.9 + - + +
92F LEU* 2.7 35.2 + - - +
94F VAL* 1.3 73.9 - - + +
96F HIS* 1.3 66.3 + - + +
97F GLU 4.7 0.8 - - - +
99F ARG* 2.9 29.3 + - - +
160F HEM 3.5 41.0 - - + +
73G ARG* 6.1 0.4 - - - +
101G GLN* 4.6 1.4 + - - -
160G HEM 3.8 18.4 + - - +
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Residues in contact with HIS 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92F LEU* 3.1 19.7 + - + +
93F GLN 3.8 6.1 - - - +
94F VAL 2.7 2.6 + - - -
95F GLN* 1.3 85.7 - - + +
97F GLU* 1.3 67.3 + - - +
98F GLY 3.3 0.2 + - - -
99F ARG* 3.0 29.8 + - - +
101F ILE* 3.7 18.5 - - + +
106F PHE* 4.8 3.6 - + + -
141F ILE* 4.1 21.2 - - + +
160F HEM 1.9 95.5 + + + -
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Residues in contact with GLU 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93F GLN* 2.9 27.1 + - + +
94F VAL* 3.4 35.1 - - - +
95F GLN 4.7 1.0 - - - -
96F HIS* 1.3 75.2 - - - +
98F GLY* 1.3 60.1 + - - +
99F ARG* 3.6 2.6 + - - +
141F ILE 5.5 0.6 + - - -
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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