Contacts of the helix formed by residues 63 - 82 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D ARG* 3.8 25.8 - - - +
60D ASN* 2.6 39.9 + - - +
61D ILE 3.9 0.5 - - - +
62D TYR* 1.3 77.6 - - - +
64D PRO* 1.3 69.4 - - - +
65D GLU 3.7 1.6 + - - -
66D PHE* 3.2 17.2 + - - +
67D GLY* 2.8 25.3 + - - -
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Residues in contact with PRO 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LEU* 4.1 39.9 - - + +
89A VAL* 4.2 13.1 - - + +
92A SER* 4.5 5.2 + - - -
62D TYR 3.8 1.5 - - - +
63D SER* 1.3 87.9 - - - +
65D GLU* 1.3 79.8 + - - +
67D GLY 4.2 0.2 - - - +
68D ALA* 2.8 33.3 + - - +
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Residues in contact with GLU 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A SER* 4.3 18.5 + - - +
55D ARG 5.8 1.8 - - - +
56D VAL* 4.3 13.9 - - - +
57D ARG* 3.2 44.1 + - + -
63D SER* 3.3 0.6 - - - +
64D PRO* 1.3 102.7 - - - +
66D PHE* 1.3 61.8 + - - +
68D ALA* 3.4 4.9 - - - +
69D HIS* 3.3 17.0 + - - +
72D ARG* 4.6 1.0 + - - -
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Residues in contact with PHE 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D LEU* 5.4 2.7 - - + -
39D TRP* 3.7 42.8 - + + -
43D ILE* 4.6 4.0 - - + -
53D PHE* 4.1 17.7 - + - -
56D VAL* 3.3 18.3 + - + -
57D ARG 3.4 18.2 - - - +
58D GLY* 4.0 8.5 - - - -
60D ASN 3.8 3.4 - - - +
61D ILE* 3.2 46.2 - - + +
63D SER* 3.2 10.8 + - - +
65D GLU* 1.3 76.4 - - - +
67D GLY* 1.3 56.6 + - - +
69D HIS* 2.9 28.4 + + - +
70D SER* 2.7 39.0 + - - -
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Residues in contact with GLY 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A VAL* 4.1 15.4 - - - +
32D VAL* 5.4 8.9 - - - +
61D ILE 4.3 5.1 + - - -
63D SER 2.8 18.5 + - - -
64D PRO 3.1 2.4 + - - -
66D PHE* 1.3 78.0 - - - +
68D ALA* 1.3 63.2 + - - +
70D SER* 3.2 9.4 - - - -
71D GLN* 3.0 24.1 + - - +
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Residues in contact with ALA 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A VAL* 3.5 17.8 - - + +
92A SER* 3.9 15.9 - - - +
93A HIS* 4.0 14.7 - - + +
64D PRO 2.8 15.6 + - - +
65D GLU 3.4 10.8 - - - +
67D GLY* 1.3 74.5 - - - +
69D HIS* 1.3 66.5 + - - +
71D GLN* 2.9 11.6 + - - +
72D ARG* 3.0 31.8 + - - +
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Residues in contact with HIS 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D TRP* 4.8 2.2 - - - -
53D PHE* 3.3 13.1 - + - -
56D VAL* 3.8 21.1 - - + -
65D GLU 3.3 1.6 + - - +
66D PHE* 2.9 33.1 + + - +
68D ALA* 1.3 78.2 - - - +
70D SER* 1.3 68.7 + - - +
72D ARG* 2.8 43.9 + - - +
73D VAL* 2.9 24.4 + - + +
160D HEM 3.8 40.0 + + + +
161D CMO 2.9 28.7 + - - -
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Residues in contact with SER 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D VAL* 4.8 1.9 + - - +
35D GLY* 3.4 31.9 - - - -
36D LEU* 3.9 2.2 + - - -
39D TRP* 3.7 22.8 - - - +
66D PHE* 2.7 20.5 + - - -
67D GLY* 3.2 14.8 - - - -
69D HIS* 1.3 74.3 - - - +
71D GLN* 1.3 65.9 + - - +
73D VAL* 3.2 3.5 - - - +
74D LEU* 2.9 29.9 + - - +
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Residues in contact with GLN 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A LEU* 3.7 19.7 - - + +
82A ASN 5.8 0.6 + - - -
83A LEU* 3.5 30.7 - - + +
89A VAL* 5.1 1.9 - - + +
25D PHE* 4.4 9.5 - - - -
28D ALA 5.0 0.2 + - - -
31D ARG* 3.1 41.9 + - - +
32D VAL* 3.3 31.8 - - + +
35D GLY* 5.2 0.5 - - - +
67D GLY 3.0 9.1 + - - +
68D ALA* 2.9 12.6 + - - +
70D SER* 1.3 83.6 + - - +
72D ARG* 1.3 66.6 + - - +
73D VAL 3.0 0.3 + - - -
74D LEU* 3.2 5.8 + - - +
75D SER* 2.8 24.4 + - - -
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Residues in contact with ARG 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LEU* 4.6 4.7 - - + +
92A SER* 5.3 0.6 + - - -
93A HIS* 3.4 29.7 + - + +
96A HIS* 3.3 55.9 + - - +
55D ARG* 4.4 2.6 - - - +
56D VAL* 3.7 17.4 - - - +
65D GLU 4.6 0.8 + - - -
68D ALA* 3.0 35.3 + - - +
69D HIS* 2.8 42.3 + - - +
71D GLN* 1.3 71.9 - - - +
73D VAL* 1.3 66.3 + - + +
75D SER* 3.3 8.0 - - - -
76D GLY 3.1 14.9 + - - -
160D HEM 4.0 32.2 + - + +
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Residues in contact with VAL 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D TRP* 4.0 15.0 - - + +
69D HIS* 2.9 32.9 + - + +
70D SER* 3.2 9.0 - - - +
72D ARG* 1.3 72.7 - - - +
74D LEU* 1.3 76.1 + - + +
76D GLY* 2.8 14.9 + - - -
77D LEU* 3.0 10.6 + - + +
114D PHE* 4.6 7.2 - - + -
160D HEM 3.9 31.2 - - + +
161D CMO 3.2 37.0 - - - +
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Residues in contact with LEU 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D TRP* 3.8 20.4 - - + -
25D PHE* 3.7 25.6 - - + -
34D PHE* 3.8 30.5 - - + -
35D GLY* 4.1 20.9 - - - -
38D LEU* 4.5 10.3 - - + -
39D TRP* 4.2 8.7 - - - +
70D SER* 2.9 27.7 + - - +
71D GLN* 3.7 9.9 - - - +
73D VAL* 1.3 86.6 - - + +
75D SER* 1.3 52.8 + - - +
77D LEU* 2.9 18.6 + - + +
78D ASP* 2.7 33.3 + - - +
114D PHE* 5.8 0.9 - - + -
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Residues in contact with SER 75 (chain D).
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* 3.7 30.1 + - - +
76A GLY* 5.4 0.3 - - - -
78A LYS* 5.8 0.7 - - - +
79A LEU* 3.9 21.7 - - - +
25D PHE* 4.7 5.0 - - - -
31D ARG* 6.3 0.9 - - - +
71D GLN 2.8 13.3 + - - -
72D ARG* 3.3 11.9 - - - -
74D LEU* 1.3 76.1 - - - +
76D GLY* 1.3 58.5 - - - +
78D ASP* 2.8 25.9 + - - +
79D ILE* 2.9 15.6 + - - +
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Residues in contact with GLY 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D ARG 3.1 6.2 + - - -
73D VAL 2.8 10.6 + - - -
75D SER* 1.3 75.1 - - - +
77D LEU* 1.3 63.4 + - - +
79D ILE* 3.0 18.6 + - - +
80D THR* 2.9 29.5 + - - +
93D GLN* 4.9 4.2 + - - -
97D LEU* 5.2 2.5 - - - -
160D HEM 4.4 17.3 - - - -
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Residues in contact with LEU 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D TRP* 3.9 22.2 - - + -
73D VAL 3.0 7.3 + - - +
74D LEU* 2.9 23.6 + - + +
76D GLY* 1.3 74.8 - - - +
78D ASP* 1.3 60.8 + - - +
80D THR* 2.6 28.7 + - - +
81D ILE* 3.0 31.9 + - + +
114D PHE* 4.4 11.4 - - + -
118D LEU* 3.5 36.6 - - + -
139D VAL* 5.0 6.1 - - + -
142D ILE* 4.8 8.5 - - + -
160D HEM 3.9 28.5 - - + +
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Residues in contact with ASP 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A TRP* 5.0 1.9 + - - -
31A ARG* 4.2 9.2 + - - -
75A ASN* 3.6 15.2 + - - +
78A LYS* 4.6 6.4 + - - -
21D TRP* 3.3 33.6 + - + +
25D PHE* 4.0 15.7 - - + -
31D ARG* 4.4 6.6 + - - -
74D LEU 2.7 11.9 + - - +
75D SER* 2.8 16.7 + - - +
77D LEU* 1.3 77.6 - - - +
79D ILE* 1.3 61.1 + - - +
81D ILE* 3.2 2.6 + - - +
82D SER* 2.8 28.2 + - - -
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Residues in contact with ILE 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A VAL* 3.5 23.3 - - + -
72A ARG* 4.1 24.7 - - + +
75A ASN* 3.1 40.2 - - + +
75D SER* 2.9 7.1 + - - +
76D GLY* 3.3 18.4 - - - +
78D ASP* 1.3 75.6 + - - +
80D THR* 1.3 67.8 + - - +
82D SER* 2.6 25.9 + - - -
83D MET* 3.1 24.5 + - - +
93D GLN* 4.0 17.0 - - - +
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Residues in contact with THR 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D GLY 2.9 14.1 + - - +
77D LEU* 2.6 26.7 + - - +
79D ILE* 1.3 72.4 - - - +
81D ILE* 1.3 55.3 + - - +
83D MET* 2.7 28.8 + - - +
84D LEU* 2.9 15.5 + - - +
90D LEU* 3.9 9.6 - - - +
93D GLN* 4.2 10.5 - - + -
94D LEU* 4.3 3.8 - - + -
97D LEU* 3.6 28.9 - - + -
142D ILE* 3.4 35.8 - - + +
160D HEM 5.0 1.1 - - + -
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Residues in contact with ILE 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D VAL* 4.0 20.4 - - + -
18D LYS* 3.1 29.3 + - - +
21D TRP* 3.7 38.6 - - + -
77D LEU* 3.0 32.8 + - + +
78D ASP* 3.5 4.9 - - - +
80D THR* 1.3 84.8 + - - +
82D SER* 1.3 57.4 + - - +
83D MET 3.0 4.2 + - - -
84D LEU* 3.4 24.7 + - + +
135D TRP* 4.0 19.7 - - + -
139D VAL* 5.1 2.0 - - + -
142D ILE* 4.1 10.5 - - + -
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Residues in contact with SER 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A SER* 3.6 15.7 - - - -
28A THR* 3.2 21.9 + - - +
31A ARG* 3.3 31.9 + - - -
71A VAL* 5.0 0.2 - - - +
18D LYS* 3.1 19.0 + - - +
78D ASP* 2.8 15.7 + - - -
79D ILE* 2.6 28.3 + - - +
81D ILE* 1.3 71.6 - - - +
83D MET* 1.3 58.5 + - - +
85D ASP* 3.4 5.2 - - - +
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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
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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