Contacts of the helix formed by residues 64 - 82 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLU 3.1 5.4 + - - -
63A SER* 1.3 80.7 + - - +
65A GLU* 1.3 58.8 + - - +
66A PHE 3.0 1.5 - - - +
67A LYS* 3.6 25.0 - - - +
68A SER* 2.9 30.5 + - - -
88D ASP* 4.1 12.3 - - - -
89D MET* 4.3 6.1 - - - -
92D ALA* 3.8 8.1 - - - +
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Residues in contact with GLU 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A VAL* 3.6 19.3 - - - +
57A LYS* 3.9 33.9 + - + -
60A GLU* 6.0 0.2 - - - +
63A SER* 3.5 17.2 + - - +
64A GLY* 1.3 77.2 - - - +
66A PHE* 1.3 56.9 + - - +
68A SER* 3.0 15.1 + - - -
69A HIS* 3.7 6.9 + - - +
72A ARG* 4.2 3.3 + - - -
88D ASP 5.3 1.9 - - - +
92D ALA* 4.2 18.5 - - + +
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Residues in contact with PHE 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ARG* 3.7 23.3 - - + -
39A PHE* 5.8 2.7 - + + -
43A PHE* 5.2 11.0 - + - -
53A PHE* 5.0 1.8 - + + -
56A VAL* 3.4 29.6 - - + +
57A LYS 3.5 7.4 - - - +
58A ILE* 3.2 31.9 - - + -
60A GLU 4.3 0.2 - - - -
61A PRO* 3.3 27.8 - - + -
63A SER* 2.8 18.1 + - - +
65A GLU* 1.3 78.1 - - - +
67A LYS* 1.3 66.1 + - - +
68A SER 3.2 1.1 - - - -
69A HIS* 2.8 36.8 + + - +
70A LEU* 3.0 29.0 + - + +
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Residues in contact with LYS 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A VAL* 4.8 12.6 - - + +
36A ARG* 4.0 10.5 - - - +
61A PRO 3.9 16.6 - - - +
62A GLU* 3.6 31.8 + - - +
64A GLY* 3.5 12.7 + - - +
66A PHE* 1.3 76.7 - - - +
68A SER* 1.3 64.0 + - - +
70A LEU* 2.9 24.2 + - - +
71A VAL* 3.0 13.2 + - - +
86D THR* 5.9 3.4 - - - +
88D ASP* 3.5 27.2 + - - -
89D MET* 3.5 27.3 - - + -
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Residues in contact with SER 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLY 2.9 15.9 + - - -
65A GLU* 3.0 13.9 + - - -
67A LYS* 1.3 75.7 - - - +
69A HIS* 1.3 66.2 + - - +
71A VAL* 3.1 5.7 + - - +
72A ARG* 2.9 42.4 + - - -
83D MET* 3.6 27.8 - - - +
89D MET* 3.5 12.6 - - - +
92D ALA* 4.2 7.1 - - - +
93D GLN* 4.3 8.1 + - - +
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Residues in contact with HIS 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A PHE* 4.7 2.9 - + - -
53A PHE* 3.4 19.5 - + - -
56A VAL* 3.9 11.9 - - + +
65A GLU 4.0 6.3 - - - +
66A PHE* 2.8 36.6 + + - +
68A SER* 1.3 80.9 + - - +
70A LEU* 1.3 71.6 + - + +
72A ARG* 2.7 48.5 + - - +
73A VAL* 2.9 22.8 + - + +
160A HEM 3.7 28.4 - + + +
161A CMO 3.3 27.0 + - - -
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Residues in contact with LEU 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A VAL* 4.3 13.7 - - + -
35A VAL* 3.7 16.2 - - + +
36A ARG* 4.1 36.8 - - + +
39A PHE* 3.5 33.2 - - + -
66A PHE* 3.0 43.1 + - + +
67A LYS* 2.9 19.0 + - - +
69A HIS* 1.3 78.8 - - + +
71A VAL* 1.3 58.8 + - + +
73A VAL* 3.0 10.8 + - - +
74A ALA* 2.8 28.6 + - - +
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Residues in contact with VAL 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A THR* 4.0 11.4 - - + -
31A ARG* 4.4 14.4 - - - +
32A VAL* 3.8 17.7 - - + +
67A LYS 3.0 2.7 + - - +
68A SER 3.2 7.2 - - - +
70A LEU* 1.3 75.3 - - - +
72A ARG* 1.3 54.8 + - - +
74A ALA* 3.0 8.1 + - - +
75A ASN* 2.6 45.7 + - - +
79D ILE* 3.5 28.7 - - + -
82D SER* 5.0 0.4 - - - +
83D MET* 4.3 4.0 - - + -
89D MET* 3.3 33.9 - - + -
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Residues in contact with ARG 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ARG* 5.1 1.0 - - - +
56A VAL* 4.3 4.6 - - - +
65A GLU 4.2 3.4 + - - -
68A SER* 2.9 36.5 + - - +
69A HIS* 2.7 43.0 + - - +
71A VAL* 1.3 72.4 - - - +
73A VAL* 1.3 52.0 + - + +
75A ASN* 3.7 0.9 - - - +
76A GLY* 2.8 30.7 + - - -
160A HEM 3.7 48.3 + - + +
79D ILE* 4.1 22.1 - - + +
92D ALA 5.7 0.4 + - - -
93D GLN* 2.8 29.9 + - - +
96D HIS* 3.5 41.1 + - + +
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Residues in contact with VAL 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A VAL* 4.3 7.0 - - + -
39A PHE* 4.0 19.5 - - + -
69A HIS* 2.9 32.7 + - + +
70A LEU* 3.2 8.5 - - - +
72A ARG* 1.3 72.0 - - + +
74A ALA* 1.3 72.7 + - - +
76A GLY* 3.0 9.5 + - - -
77A LEU* 3.0 12.7 + - + +
119A PHE* 6.0 4.9 - - + -
160A HEM 4.0 34.8 - - + +
161A CMO 3.2 28.9 - - - +
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Residues in contact with ALA 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A TRP* 4.5 1.3 - - - -
23A TRP* 3.2 28.3 - - + -
31A ARG* 4.6 4.9 - - + -
35A VAL* 3.2 30.9 - - + +
70A LEU 2.8 9.5 + - - +
71A VAL* 3.2 11.9 - - - +
73A VAL* 1.3 75.0 - - - +
75A ASN* 1.3 55.8 + - - +
77A LEU* 2.7 31.1 + - - +
78A LYS* 2.8 11.3 + - - +
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Residues in contact with ASN 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TRP* 3.1 11.2 - - - -
31A ARG* 3.1 24.9 + - - -
71A VAL* 2.6 22.2 + - - +
72A ARG 3.9 0.4 - - - +
74A ALA* 1.3 73.2 - - - +
76A GLY* 1.3 57.6 + - - +
78A LYS* 3.3 11.7 - - - +
79A LEU* 2.8 30.3 + - - +
75D SER* 3.7 21.2 + - - +
78D ASP* 3.6 20.4 + - - -
79D ILE* 3.1 40.0 - - + +
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Residues in contact with GLY 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ARG 2.8 20.2 + - - -
73A VAL 3.0 4.6 + - - -
75A ASN* 1.3 73.5 - - - +
77A LEU* 1.3 60.7 + - - +
79A LEU* 3.6 7.7 - - - +
80A LEU* 3.3 24.4 + - - +
93A HIS* 4.5 5.4 + - - -
97A LEU* 5.0 5.0 - - - +
160A HEM 4.3 20.2 - - - -
75D SER* 5.4 0.4 - - - -
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Residues in contact with LEU 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A TRP* 3.8 23.8 - - + -
35A VAL* 6.3 0.9 - - + -
73A VAL* 3.0 10.4 + - + +
74A ALA* 2.7 13.3 + - - +
76A GLY* 1.3 72.9 - - - +
78A LYS* 1.3 69.2 + - - +
80A LEU* 2.9 29.5 + - + +
81A ILE* 3.0 25.9 + - + +
119A PHE* 3.4 42.6 - - + -
135A TRP* 4.5 3.1 - - + -
139A PHE* 4.2 23.8 - - + -
142A LEU* 5.1 2.5 - - + -
160A HEM 4.1 15.8 - - + +
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Residues in contact with LYS 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A TRP* 3.2 36.5 - - + +
23A TRP* 3.0 40.4 - - + +
74A ALA 2.8 11.0 + - - +
75A ASN* 3.3 20.2 - - - +
77A LEU* 1.3 77.0 - - - +
79A LEU* 1.3 58.3 + - - +
81A ILE* 3.3 1.0 + - - +
82A ASN* 2.8 46.1 + - - +
27D HIS* 5.3 6.8 + - - -
31D ARG* 2.8 44.0 - - - +
75D SER* 5.8 0.7 - - - +
78D ASP* 4.6 7.7 + - - -
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Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A ASN 2.8 19.7 + - - +
76A GLY* 3.6 9.4 - - - +
78A LYS* 1.3 77.0 - - - +
80A LEU* 1.3 63.7 + - - +
82A ASN* 3.6 5.4 + - + -
83A LEU* 3.3 29.8 + - + +
93A HIS* 3.5 38.8 - - + +
25D PHE* 6.3 1.3 - - + -
31D ARG* 5.1 9.4 - - - +
71D GLN* 3.7 36.6 - - + +
72D ARG* 4.8 3.1 - - - +
75D SER* 3.9 28.3 - - - +
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Residues in contact with LEU 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLY 3.3 13.7 + - - +
77A LEU* 2.9 20.8 + - + +
79A LEU* 1.3 79.0 - - - +
81A ILE* 1.3 54.6 - - - +
83A LEU* 2.7 34.5 + - - +
84A LEU* 3.4 7.4 + - - +
90A LEU* 3.9 12.8 - - + +
93A HIS* 3.6 22.4 - - + -
94A LEU* 3.3 30.5 - - + -
97A LEU* 3.8 20.9 - - + -
139A PHE* 6.3 0.7 - - + -
142A LEU* 4.3 24.2 - - + -
146A ILE* 4.4 5.8 - - + -
160A HEM 4.3 7.6 - - + -
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Residues in contact with ILE 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ILE* 4.0 26.5 - - + -
16A ARG* 4.5 15.5 - - + +
19A TRP* 3.3 62.8 - - + -
77A LEU* 3.0 15.6 + - + +
78A LYS 3.7 5.6 - - - +
80A LEU* 1.3 78.0 - - + +
82A ASN* 1.3 58.9 + - - +
83A LEU 2.8 10.6 + - - -
84A LEU* 3.0 38.4 + - + +
135A TRP* 4.0 11.4 - - + -
142A LEU* 5.2 5.6 - - + -
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Residues in contact with ASN 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ARG* 5.3 8.4 - - - +
19A TRP* 4.9 2.6 - - - -
20A ASP* 5.1 2.9 - - - +
78A LYS* 2.8 34.0 + - - +
79A LEU* 3.6 6.5 - - + +
80A LEU 3.2 0.2 + - - -
81A ILE* 1.3 76.5 - - - +
83A LEU* 1.3 65.2 + - + +
84A LEU 3.7 0.2 - - - -
85A ASP* 5.2 0.8 - - - +
86A ASP* 5.0 1.0 - - - +
27D HIS* 3.7 13.3 - - - +
28D ALA* 3.2 45.4 + - - +
31D ARG* 2.8 49.8 - - - +
71D GLN* 5.8 0.7 + - - -
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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