Contacts of the helix formed by residues 64 - 82 (chain I) 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 GLY 64 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62I GLU 3.1 5.4 + - - -
63I SER* 1.3 81.1 + - - +
65I GLU* 1.3 62.3 + - - +
66I PHE 2.9 2.4 - - - +
67I LYS* 3.6 25.4 - - - +
68I SER* 2.9 26.5 + - - -
88L ASP* 4.2 11.2 - - - -
89L MET* 4.3 6.9 - - - -
92L ALA* 4.0 8.5 - - - +
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Residues in contact with GLU 65 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56I VAL* 3.6 19.6 - - - +
57I LYS* 3.9 34.2 + - + -
60I GLU* 6.0 0.2 - - - +
63I SER* 3.5 17.6 + - - +
64I GLY* 1.3 76.7 - - - +
66I PHE* 1.3 58.1 + - - +
68I SER* 3.0 15.9 + - - -
69I HIS* 3.7 6.8 + - - +
72I ARG* 4.2 3.1 + - - -
88L ASP 5.1 2.8 - - - +
92L ALA* 4.2 21.0 - - + +
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Residues in contact with PHE 66 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36I ARG* 3.7 22.7 - - + -
39I PHE* 5.7 2.9 - + + -
43I PHE* 5.3 10.5 - + - -
53I PHE* 5.0 1.3 - + + -
56I VAL* 3.4 28.9 - - + +
57I LYS 3.5 7.0 - - - +
58I ILE* 3.2 32.1 - - + -
61I PRO* 3.3 27.8 - - + -
63I SER* 2.8 17.8 + - - +
65I GLU* 1.3 76.8 - - - +
67I LYS* 1.3 64.6 + - - +
68I SER 3.2 1.1 - - - -
69I HIS* 2.8 37.6 + + - +
70I LEU* 2.9 29.3 + - + +
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Residues in contact with LYS 67 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32I VAL* 4.8 13.4 - - + +
36I ARG* 4.0 10.5 - - - +
61I PRO 3.9 16.8 - - - +
62I GLU* 3.7 36.0 + - - +
64I GLY* 3.5 11.0 + - - +
66I PHE* 1.3 77.6 - - - +
68I SER* 1.3 64.0 + - - +
70I LEU* 2.9 24.3 + - - +
71I VAL* 3.0 13.0 + - - +
86L THR* 5.8 3.6 - - - +
88L ASP* 4.0 17.9 + - - -
89L MET* 3.4 31.1 - - + -
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Residues in contact with SER 68 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64I GLY 2.9 16.2 + - - -
65I GLU* 3.0 14.2 + - - -
67I LYS* 1.3 75.0 - - - +
69I HIS* 1.3 68.0 + - - +
71I VAL* 3.1 6.3 + - - +
72I ARG* 2.9 40.8 + - - +
83L MET* 3.6 30.0 - - - +
89L MET* 3.5 9.5 - - - +
92L ALA* 4.5 3.3 - - - +
93L GLN* 4.2 12.0 + - - +
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Residues in contact with HIS 69 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39I PHE* 4.7 2.5 - + - -
53I PHE* 3.4 19.7 - + - -
56I VAL* 3.9 12.3 - - + +
65I GLU 4.0 6.7 - - - +
66I PHE* 2.8 39.1 + + - +
68I SER* 1.3 80.5 + - - +
70I LEU* 1.3 70.2 + - + -
72I ARG* 2.6 48.5 + - - +
73I VAL* 2.9 21.3 + - + +
160I HEM 3.7 27.5 - + + +
161I CMO 3.3 27.7 + - - -
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Residues in contact with LEU 70 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32I VAL* 4.3 14.4 - - + -
35I VAL* 3.7 18.2 - - + +
36I ARG* 4.1 36.3 - - + +
39I PHE* 3.5 33.2 - - + -
66I PHE* 2.9 43.8 + - + +
67I LYS* 2.9 22.4 + - - +
69I HIS* 1.3 75.5 - - + +
71I VAL* 1.3 58.8 + - + +
73I VAL* 3.0 10.0 + - - +
74I ALA* 2.8 28.6 + - - +
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Residues in contact with VAL 71 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28I THR* 4.0 13.7 - - + -
31I ARG* 4.5 14.1 - - - +
32I VAL* 3.8 19.7 - - + +
67I LYS 3.0 11.7 + - - +
68I SER* 3.2 9.0 - - - +
70I LEU* 1.3 76.5 - - - +
72I ARG* 1.3 54.5 + - - +
74I ALA* 2.9 8.4 + - - +
75I ASN* 2.6 47.8 + - - +
79L ILE* 3.6 27.8 - - + -
82L SER* 5.1 0.2 - - - +
83L MET* 4.5 1.3 - - + -
89L MET* 3.7 20.9 - - + -
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Residues in contact with ARG 72 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55I ARG* 5.1 1.0 - - - +
56I VAL* 4.3 4.4 - - - +
65I GLU 4.2 3.4 + - - -
68I SER* 2.9 35.9 + - - +
69I HIS* 2.6 42.8 + - - +
71I VAL* 1.3 71.7 - - - +
73I VAL* 1.3 57.7 + - + +
75I ASN* 3.5 0.9 + - - +
76I GLY* 2.8 26.3 + - - -
160I HEM 3.7 51.2 + - + +
79L ILE* 4.0 21.8 - - + -
93L GLN* 3.0 27.4 + - - +
96L HIS* 3.5 40.4 + - + +
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Residues in contact with VAL 73 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35I VAL* 4.3 7.6 - - + -
39I PHE* 4.0 18.6 - - + -
69I HIS* 2.9 32.3 + - + +
70I LEU* 3.2 8.3 - - - +
72I ARG* 1.3 74.0 - - + +
74I ALA* 1.3 71.4 + - - +
76I GLY* 3.0 9.4 + - - -
77I LEU* 3.0 13.4 + - + +
115I ILE* 5.5 3.1 - - + -
119I PHE* 6.0 4.5 - - + -
160I HEM 4.0 32.3 - - + +
161I CMO 3.2 29.2 - - - +
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Residues in contact with ALA 74 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I TRP* 5.7 0.9 - - - -
23I TRP* 3.2 27.5 - - + -
31I ARG* 4.6 4.9 - - + -
35I VAL* 3.3 30.5 - - + +
70I LEU 2.8 8.9 + - - +
71I VAL* 3.2 12.3 - - - +
73I VAL* 1.3 75.4 - - - +
75I ASN* 1.3 55.2 + - - +
77I LEU* 2.7 33.0 + - - +
78I LYS* 2.8 10.4 + - - +
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Residues in contact with ASN 75 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I TRP* 3.1 11.8 - - - +
31I ARG* 3.0 25.5 + - - -
71I VAL* 2.6 26.1 + - - +
72I ARG 3.9 1.3 - - - +
74I ALA* 1.3 73.1 - - - +
76I GLY* 1.3 56.8 + - - +
78I LYS* 3.3 12.7 - - - +
79I LEU* 2.8 30.1 + - - +
75L SER* 3.4 25.3 + - - +
78L ASP* 3.8 16.6 + - - -
79L ILE* 3.4 35.1 - - + +
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Residues in contact with GLY 76 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72I ARG 2.8 19.4 + - - -
73I VAL 3.0 4.8 + - - -
75I ASN* 1.3 74.2 - - - +
77I LEU* 1.3 60.7 + - - +
79I LEU* 3.6 7.7 + - - +
80I LEU* 3.3 24.4 + - - +
93I HIS* 4.5 5.8 + - - -
97I LEU* 5.0 4.1 - - - +
160I HEM 4.3 21.3 - - - +
75L SER* 5.5 0.4 - - - -
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Residues in contact with LEU 77 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I TRP* 3.8 23.6 - - + -
35I VAL* 6.3 1.1 - - + -
73I VAL* 3.0 9.5 + - + +
74I ALA* 2.7 12.9 + - - +
76I GLY* 1.3 74.9 - - - +
78I LYS* 1.3 67.1 + - - +
80I LEU* 2.9 29.3 + - + +
81I ILE* 3.0 27.0 + - + +
119I PHE* 3.4 42.4 - - + -
135I TRP* 4.6 2.5 - - + -
139I PHE* 4.1 24.0 - - + -
142I LEU* 5.1 2.7 - - + -
160I HEM 4.1 16.0 - - + +
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Residues in contact with LYS 78 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I TRP* 3.2 36.5 - - + +
23I TRP* 3.0 41.4 - - + +
74I ALA 2.8 10.8 + - - +
75I ASN* 3.3 19.9 - - - +
77I LEU* 1.3 77.7 - - - +
79I LEU* 1.3 63.8 + - - +
81I ILE* 3.2 1.4 + - - +
82I ASN* 2.8 42.2 + - - +
27L HIS* 5.2 6.6 + - - -
31L ARG* 2.7 44.4 - - - +
75L SER* 5.8 0.7 - - - +
78L ASP* 5.0 4.4 + - - -
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Residues in contact with LEU 79 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75I ASN 2.8 19.9 + - - +
76I GLY* 3.6 9.2 - - - +
77I LEU 3.2 0.2 - - - -
78I LYS* 1.3 76.3 - - - +
80I LEU* 1.3 66.1 + - - +
82I ASN* 3.6 5.8 + - + -
83I LEU* 3.3 28.3 + - + +
93I HIS* 3.6 37.7 - - + +
25L PHE* 6.5 0.9 - - + -
31L ARG* 5.3 8.3 - - - +
68L ALA 5.7 0.2 - - - +
71L GLN* 3.4 45.1 - - + +
72L ARG* 4.8 6.3 - - + +
75L SER* 4.2 16.2 - - - +
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Residues in contact with LEU 80 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76I GLY 3.3 13.4 + - - +
77I LEU* 2.9 24.6 + - + +
79I LEU* 1.3 78.0 - - - +
81I ILE* 1.3 54.8 + - - +
83I LEU* 2.7 34.0 + - - +
84I LEU* 3.4 7.2 + - - +
90I LEU* 3.9 12.9 - - + +
93I HIS* 3.6 24.0 - - + +
94I LEU* 3.3 31.6 - - + -
97I LEU* 3.8 20.0 - - + -
139I PHE* 6.3 0.7 - - + -
142I LEU* 4.3 21.5 - - + -
146I ILE* 4.4 6.5 - - + -
160I HEM 4.3 7.9 - - + -
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Residues in contact with ILE 81 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I ILE* 4.0 31.4 - - + -
16I ARG* 4.5 15.7 - - + +
19I TRP* 3.3 61.5 - - + -
77I LEU* 3.0 15.8 + - + +
78I LYS 3.7 6.3 - - - +
80I LEU* 1.3 78.6 - - + +
82I ASN* 1.3 58.8 + - - +
83I LEU 2.7 11.3 + - - -
84I LEU* 3.0 33.4 + - + +
85I ASP 4.9 0.2 + - - -
135I TRP* 4.0 11.7 - - + -
142I LEU* 5.2 5.8 - - + -
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Residues in contact with ASN 82 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16I ARG* 5.3 7.3 - - - +
19I TRP* 4.9 2.8 - - - -
20I ASP* 5.1 4.0 - - - +
78I LYS* 2.8 37.7 + - - +
79I LEU* 3.7 7.0 - - + +
81I ILE* 1.3 77.6 - - - +
83I LEU* 1.3 65.2 + - + +
84I LEU 3.6 0.4 - - - -
85I ASP* 5.1 1.7 - - - +
86I ASP* 5.0 2.9 - - - +
27L HIS* 3.8 9.9 - - - +
28L ALA* 2.9 52.2 + - - +
31L ARG* 3.1 38.0 - - - +
32L VAL* 5.5 1.0 - - - +
71L GLN* 5.9 0.3 + - - -
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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