Contacts of the helix formed by residues 27 - 47 (chain G) 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 GLU 27 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E SER* 3.5 28.2 - - - +
27E PHE* 3.9 26.7 - - + +
29E ASP* 4.1 12.2 - - - +
30E ARG* 3.9 25.3 + - - +
13F LYS* 3.0 25.6 + - - +
80F ASP* 4.2 6.8 - - - +
25G ASP* 3.0 9.6 + - - +
26G THR* 1.3 79.6 + - - +
28G SER* 1.3 62.9 + - - +
29G SER* 3.2 10.7 + - - -
30G LYS* 3.3 19.6 + - + +
31G ILE* 3.4 12.8 + - - +
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Residues in contact with SER 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73F ASP* 5.2 1.2 + - - -
77F SER* 4.2 15.8 - - - -
23G TRP* 4.6 18.6 - - - -
25G ASP 3.6 9.5 + - - -
26G THR 2.9 10.9 + - - -
27G GLU* 1.3 75.6 - - - +
29G SER* 1.3 58.0 + - - +
31G ILE* 3.0 9.2 + - - +
32G LYS* 2.7 59.6 + - - +
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Residues in contact with SER 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F LYS* 3.6 11.3 + - - +
77F SER* 3.1 31.9 + - - -
78F THR* 4.2 8.7 - - - -
81F GLN* 3.0 23.5 + - - -
26G THR 4.8 0.2 + - - -
27G GLU* 3.7 5.2 + - - -
28G SER* 1.3 80.5 + - - +
30G LYS* 1.3 71.8 + - - +
32G LYS* 4.6 1.3 - - - -
33G ILE* 2.8 34.2 + - - +
72G LEU* 4.6 10.3 - - - -
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Residues in contact with LYS 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E PHE* 3.6 35.0 - - + -
29E ASP* 3.5 30.8 + - - +
80F ASP* 5.5 0.8 + - - -
81F GLN* 3.5 32.2 + - - +
27G GLU* 3.3 18.8 + - + +
29G SER* 1.3 81.7 + - - +
31G ILE* 1.3 57.1 + - - +
33G ILE* 4.0 6.4 - - + +
34G GLY* 3.1 24.6 + - - -
85H ASP* 4.8 5.2 - - + +
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Residues in contact with ILE 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E PHE* 4.2 8.7 - - + -
22G LEU* 3.8 21.3 - - + +
23G TRP* 3.4 24.5 - - + -
25G ASP* 3.6 27.6 - - - +
27G GLU 3.4 9.2 + - - +
28G SER* 3.0 8.4 + - - +
30G LYS* 1.3 73.0 - - - +
32G LYS* 1.3 70.8 + - - +
33G ILE 2.8 1.9 + - - -
34G GLY* 2.9 2.6 + - - -
35G PHE* 2.7 29.7 + - + +
15H LEU* 3.5 50.3 - - + -
19H LEU* 4.9 1.8 - - + -
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Residues in contact with LYS 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73F ASP* 3.0 29.1 + - - -
77F SER* 5.6 2.7 + - - +
23G TRP* 3.8 32.7 - - + +
28G SER* 2.7 38.1 + - - +
29G SER* 5.1 0.9 - - - +
31G ILE* 1.3 74.4 - - - +
33G ILE* 1.3 52.8 + - - +
35G PHE* 4.6 2.0 - - - -
36G GLY* 2.7 34.7 + - - -
71G ALA 4.6 0.6 - - - +
72G LEU* 3.6 22.4 - - + -
75G LEU* 3.4 34.2 - - + +
76G ASN* 3.1 22.2 + - + +
79G ASP* 4.3 10.5 + - - -
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Residues in contact with ILE 33 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F THR* 5.3 0.2 - - + -
81F GLN* 4.1 22.0 - - - +
84F THR* 4.6 5.6 - - + -
29G SER* 2.8 23.8 + - - +
30G LYS* 4.0 6.5 - - + +
31G ILE 2.8 3.0 + - - -
32G LYS* 1.3 71.0 - - - +
34G GLY* 1.3 61.8 + - - +
37G ARG* 2.6 49.6 + - + +
68G SER* 3.9 38.6 - - - +
71G ALA* 4.0 9.3 - - + +
72G LEU* 3.4 30.7 - - + -
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Residues in contact with GLY 34 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G LYS 3.1 10.8 + - - -
31G ILE 2.9 7.3 + - - -
33G ILE* 1.3 78.5 - - - +
35G PHE* 1.3 57.0 + - - +
37G ARG* 3.3 14.1 - - - +
38G LEU* 2.9 30.0 + - - +
11H VAL* 4.4 22.7 - - - +
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Residues in contact with PHE 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G TRP* 4.7 9.0 - + - -
22G LEU* 5.4 6.5 - - + -
23G TRP* 5.8 1.1 - + - -
31G ILE* 2.7 29.3 + - + +
32G LYS* 3.8 3.6 - - - +
34G GLY* 1.3 70.9 - - - +
36G GLY* 1.3 56.0 + - - +
38G LEU* 3.2 9.7 + - + +
39G LEU* 2.8 71.8 + - + +
75G LEU* 3.8 15.5 - - + -
120G LEU* 4.4 1.1 - - + -
123G GLY* 4.3 9.6 - - - -
124G LEU* 3.8 39.3 - - + -
127G VAL* 3.9 33.4 - - + -
11H VAL* 5.0 1.0 - - - +
12H THR* 4.3 16.6 - - + -
15H LEU* 5.6 4.0 - - + +
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Residues in contact with GLY 36 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32G LYS 2.7 21.6 + - - -
33G ILE 3.6 0.2 - - - -
35G PHE* 1.3 72.1 - - - +
37G ARG* 1.3 64.5 + - - +
39G LEU* 3.3 6.2 + - - +
40G LEU* 3.0 30.4 + - - +
71G ALA* 4.4 10.3 - - - -
74G ILE* 5.5 3.4 - - - -
75G LEU* 4.2 21.3 - - - -
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Residues in contact with ARG 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33G ILE* 2.6 37.8 + - + +
34G GLY* 3.3 11.7 - - - +
36G GLY* 1.3 75.2 - - - +
38G LEU* 1.3 69.7 + - - +
40G LEU* 3.2 2.1 + - - +
41G THR* 2.9 28.8 + - - +
62G ALA* 3.5 40.8 + - + +
63G GLU* 3.3 38.0 + - - +
67G PHE* 4.2 17.0 - - + -
68G SER* 4.9 0.6 + - - -
71G ALA* 4.0 5.1 - - + +
11H VAL* 5.7 7.9 - - - +
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Residues in contact with LEU 38 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G GLY 2.9 16.8 + - - +
35G PHE* 3.5 8.3 - - + +
37G ARG* 1.3 81.8 - - - +
39G LEU* 1.3 81.2 + - + +
41G THR* 3.1 8.1 + - - -
42G LYS* 2.8 33.4 + - + +
119G ILE* 5.6 1.3 - - + -
123G GLY* 6.0 3.4 - - - -
126G GLN* 5.6 3.8 - - - +
10H LEU* 5.1 11.7 - - + -
11H VAL* 4.9 13.7 - - + -
12H THR* 3.6 32.3 - - + +
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Residues in contact with LEU 39 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35G PHE* 2.8 60.3 + - + +
36G GLY* 3.6 5.6 - - - +
38G LEU* 1.3 86.3 - - + +
40G LEU* 1.3 63.1 + - + +
42G LYS* 3.7 3.1 + - - +
43G LEU* 3.3 17.0 + - - +
74G ILE* 6.0 1.1 - - + -
75G LEU* 4.3 12.6 - - + -
78G LEU* 5.7 0.2 - - + -
116G PHE* 4.1 23.6 - - + -
119G ILE* 4.1 28.2 - - + +
120G LEU* 3.4 32.5 - - + -
123G GLY* 5.1 3.6 - - - -
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Residues in contact with LEU 40 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36G GLY 3.0 20.7 + - - +
37G ARG 3.8 2.7 - - - +
39G LEU* 1.3 72.2 - - - +
41G THR* 1.3 67.5 + - - +
43G LEU* 2.9 17.6 + - + +
44G ALA* 3.0 14.1 + - - +
54G PHE* 3.5 30.3 - - + -
59G ILE* 5.0 2.8 - - - +
67G PHE* 3.8 21.3 - - + -
70G HIS* 3.4 36.1 - - + +
71G ALA* 4.7 2.7 - - - -
74G ILE* 3.7 33.4 - - + -
116G PHE* 4.0 14.4 - - + -
160G HEM 5.8 1.1 - - + -
161G CMO 5.1 0.4 - - - -
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Residues in contact with THR 41 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37G ARG* 2.9 27.0 + - - +
38G LEU* 3.4 11.8 - - - -
40G LEU* 1.3 74.9 - - - +
42G LYS* 1.3 57.3 + - - +
43G LEU 2.8 10.2 + - - -
44G ALA* 2.8 19.6 + - + +
45G LYS* 2.8 16.4 + - + +
59G ILE* 5.5 5.4 - - - +
62G ALA* 4.8 8.3 - - - +
67G PHE* 4.9 4.6 - - - -
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Residues in contact with LYS 42 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38G LEU* 2.8 27.9 + - + +
39G LEU 4.0 3.6 - - - +
41G THR* 1.3 74.2 - - + +
43G LEU* 1.3 61.5 + - - +
45G LYS* 3.8 18.4 - - + +
46G ASP* 3.6 39.2 + - - -
119G ILE* 3.6 32.2 - - + +
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Residues in contact with LEU 43 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39G LEU 3.3 12.4 + - - +
40G LEU* 2.9 13.1 + - + +
41G THR 2.8 1.0 + - - -
42G LYS* 1.3 75.3 - - - +
44G ALA* 1.3 61.6 + - - +
45G LYS 3.0 1.6 - - - -
46G ASP* 3.1 4.3 + - - -
47G ILE* 2.9 31.6 + - + +
50G VAL* 4.2 23.8 - - + -
54G PHE* 4.7 6.1 - - + -
112G HIS* 4.1 18.4 - - + +
115G LYS* 4.1 10.1 - - + -
116G PHE* 4.1 22.0 - - + +
119G ILE* 3.6 20.6 - - + -
160G HEM 3.9 30.3 - - + -
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Residues in contact with ALA 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40G LEU 3.0 9.5 + - - +
41G THR* 2.8 9.8 + - + +
43G LEU* 1.3 76.9 - - - +
45G LYS* 1.3 62.4 + - - +
47G ILE 3.5 10.3 - - - -
48G PRO* 3.4 22.7 - - - +
50G VAL* 4.2 10.0 - - + +
51G ASN* 3.5 31.1 + - - +
59G ILE* 4.3 14.4 - - + -
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Residues in contact with LYS 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41G THR* 2.8 18.5 + - + +
42G LYS* 3.6 25.1 - - + +
44G ALA* 1.3 80.0 - - - +
46G ASP* 1.3 71.2 + - - +
47G ILE* 4.7 0.2 - - - -
48G PRO* 4.7 3.8 - - - +
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Residues in contact with ASP 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G LYS* 3.6 32.4 + - - +
43G LEU 3.1 6.9 + - - +
45G LYS* 1.3 89.6 - - - +
47G ILE* 1.3 67.2 + - + +
48G PRO* 4.1 3.9 - - - +
115G LYS* 3.0 38.5 - - + +
119G ILE* 4.8 2.1 - - - +
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Residues in contact with ILE 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43G LEU* 2.9 11.1 + - + +
44G ALA* 3.4 7.9 - - - +
45G LYS 3.4 0.2 - - - -
46G ASP* 1.3 90.9 - - + +
48G PRO* 1.3 62.1 - - + +
49G GLU* 3.5 33.0 - - + +
50G VAL* 3.0 30.6 - - + +
111G ALA* 4.4 11.9 - - + +
112G HIS* 3.7 24.5 - - + +
115G LYS* 4.1 26.9 - - + -
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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