Contacts of the helix formed by residues 27 - 46 (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 PHE 27 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A SER* 3.1 20.6 + - - +
26A SER* 1.3 86.1 - - - +
28A THR* 1.3 69.4 + - - +
29A ASP* 3.2 7.5 + - - +
30A ARG* 3.8 4.2 + - - +
31A ARG* 4.3 4.9 + - - -
25C ASP* 3.5 24.0 - - - -
27C GLU* 4.2 15.7 - - + -
30C LYS* 3.8 30.5 - - + -
31C ILE* 4.0 20.4 - - + -
15D LEU* 4.0 21.8 - - + -
18D LYS* 3.6 21.3 - - + +
82D SER 4.6 0.4 - - - -
85D ASP* 3.5 33.7 - - + -
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Residues in contact with THR 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A SER 4.2 0.2 - - - -
27A PHE* 1.3 68.9 - - - +
29A ASP* 1.3 71.9 + - - +
30A ARG 2.7 3.8 + - - -
31A ARG* 2.9 33.0 + - - +
32A VAL* 3.1 16.3 + - - -
71A VAL* 4.0 17.0 - - + -
82D SER* 3.2 29.3 + - - +
83D MET* 4.0 20.0 - - + -
85D ASP* 4.4 3.5 + - - -
86D THR* 4.0 21.8 + - - +
89D MET* 4.2 9.3 - - + -
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Residues in contact with ASP 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A PHE* 4.4 6.3 - - + +
28A THR* 1.3 82.0 + - - +
30A ARG* 1.3 65.5 + - - +
32A VAL* 3.5 6.9 - - - +
33A ALA* 3.2 20.3 + - - +
80B ASP* 5.0 8.5 - - - +
27C GLU* 4.3 17.0 - - + +
30C LYS* 3.3 41.0 + - - +
85D ASP* 4.7 6.2 - - - +
86D THR* 5.1 5.5 - - - +
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Residues in contact with ARG 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ASP* 3.4 22.3 + - - -
22A VAL* 3.0 32.8 + - - +
24A SER* 3.8 15.4 + - - -
25A SER* 4.1 13.5 - - - +
27A PHE 3.8 1.2 + - - -
28A THR 2.7 4.8 + - - -
29A ASP* 1.3 73.8 - - - +
31A ARG* 1.3 67.5 + - - +
32A VAL 2.9 1.6 + - - -
33A ALA* 3.0 15.8 + - - +
34A ILE* 3.1 28.6 + - + +
126A VAL* 3.8 21.0 + - - +
127A LEU* 5.2 0.6 - - - +
10B LEU* 4.1 32.6 + - + +
13B LYS* 6.1 2.2 - - - +
14B SER* 3.9 20.7 + - - +
26C THR* 4.4 12.8 + - - -
27C GLU* 3.6 17.8 + - - +
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Residues in contact with ARG 31 (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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22A VAL 5.0 3.8 + - - +
23A TRP* 3.4 57.7 - - + +
25A SER 3.3 23.2 + - - -
26A SER* 4.0 14.1 - - - +
27A PHE 4.3 2.6 + - - -
28A THR* 2.9 37.6 + - - +
30A ARG* 1.3 78.5 - - - +
32A VAL* 1.3 61.2 + - + +
34A ILE* 3.3 9.2 + - - +
35A VAL* 2.9 35.8 + - - +
71A VAL* 4.4 14.7 - - + +
74A ALA* 4.6 4.0 - - + -
75A ASN* 3.1 24.5 + - - -
78D ASP* 4.2 6.1 + - - -
82D SER* 3.3 27.3 + - - -
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Residues in contact with VAL 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A THR* 3.6 22.2 - - - +
29A ASP* 3.5 10.5 - - - +
30A ARG 2.9 1.2 + - - -
31A ARG* 1.3 83.4 - - - +
33A ALA* 1.3 67.6 + - - +
34A ILE 3.0 0.5 + - - -
35A VAL* 3.1 4.0 + - - +
36A ARG* 2.8 40.5 + - - +
67A LYS* 4.8 12.1 - - + +
70A LEU* 4.3 22.7 - - + +
71A VAL* 3.8 29.4 - - + +
89D MET* 4.2 9.0 - - + -
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Residues in contact with ALA 33 (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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29A ASP 3.2 9.0 + - - +
30A ARG* 3.0 8.6 + - - +
32A VAL* 1.3 81.9 - - + +
34A ILE* 1.3 56.4 + - - +
36A ARG* 3.6 10.3 - - - +
37A ALA* 2.8 30.7 + - - +
6B VAL* 5.2 10.9 - - + +
7B LEU* 5.3 1.2 - - + +
10B LEU* 4.2 21.5 - - + -
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Residues in contact with ILE 34 (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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19A TRP* 6.6 0.4 - - + -
22A VAL* 4.1 28.5 - - + +
30A ARG* 3.1 32.6 + - + +
31A ARG* 3.6 8.3 - - - +
32A VAL 3.1 0.6 - - - -
33A ALA* 1.3 73.5 - - - +
35A VAL* 1.3 72.5 + - + +
37A ALA* 3.1 8.3 + - - +
38A VAL* 2.9 32.1 + - + +
119A PHE* 5.7 2.5 - - + -
122A VAL* 4.6 7.2 - - + -
123A LEU* 4.4 20.0 - - + -
126A VAL* 4.0 31.0 - - + -
7B LEU* 5.6 0.2 - - - -
10B LEU* 4.3 8.3 - - + -
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Residues in contact with VAL 35 (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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19A TRP* 6.2 2.7 - - + -
23A TRP* 5.2 1.3 - - + -
31A ARG* 2.9 22.7 + - + +
32A VAL 3.9 2.2 - - - +
34A ILE* 1.3 75.5 - - + +
36A ARG* 1.3 64.5 + - - +
38A VAL* 3.2 12.7 - - + +
39A PHE* 3.0 41.0 + - + -
70A LEU* 3.7 25.8 - - + +
73A VAL* 4.3 7.4 - - + -
74A ALA* 3.2 34.3 - - + -
77A LEU* 6.3 0.9 - - + -
119A PHE* 5.6 10.8 - - + -
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Residues in contact with ARG 36 (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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32A VAL* 2.8 26.7 + - - +
33A ALA* 3.6 8.5 - - - +
35A VAL* 1.3 73.5 - - - +
37A ALA* 1.3 54.8 + - - +
38A VAL 2.7 14.9 + - - -
39A PHE* 2.7 16.9 + - + +
40A ASP* 2.9 31.3 + - - +
61A PRO* 3.4 32.9 + - - +
62A GLU* 3.5 25.3 + - - -
66A PHE* 3.7 22.8 - - + -
67A LYS* 4.0 14.5 - - - +
70A LEU* 4.1 24.7 - - + +
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Residues in contact with ALA 37 (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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33A ALA 2.8 21.9 + - - +
34A ILE 3.4 5.4 - - - +
36A ARG* 1.3 73.4 - - - +
38A VAL* 1.3 60.9 + - - +
40A ASP* 3.8 12.8 + - - +
41A ASP* 3.5 13.9 + - - +
122A VAL* 3.8 16.8 - - + +
6B VAL* 6.4 0.9 - - + -
7B LEU* 3.9 29.4 - - + -
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Residues in contact with VAL 38 (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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34A ILE* 2.9 25.2 + - + +
35A VAL* 3.2 11.0 - - + +
36A ARG 2.7 4.4 + - - -
37A ALA* 1.3 72.2 - - - +
39A PHE* 1.3 68.5 + - + +
41A ASP* 3.0 15.6 + - - +
42A LEU* 3.1 8.1 + - - +
115A ILE* 4.0 10.5 - - + -
118A ALA* 3.5 22.7 - - + +
119A PHE* 3.7 47.6 - - + -
122A VAL* 3.7 23.3 - - + -
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Residues in contact with PHE 39 (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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35A VAL* 3.0 35.1 + - + -
36A ARG* 2.7 13.7 + - + +
38A VAL* 1.3 77.3 - - + +
40A ASP* 1.3 54.6 + - - +
42A LEU* 2.6 45.9 + - + +
43A PHE* 2.8 39.9 + + + -
53A PHE* 4.1 17.9 - + - -
66A PHE* 5.8 2.7 - + + -
69A HIS* 4.8 2.7 - + - -
70A LEU* 3.5 21.3 - - + -
73A VAL* 4.0 17.5 - - + -
115A ILE* 3.8 24.9 - - + -
160A HEM 5.3 1.6 - + - -
161A CMO 3.4 23.8 - - - -
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Residues in contact with ASP 40 (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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36A ARG* 2.9 43.8 + - - +
37A ALA* 3.9 11.1 - - - +
39A PHE* 1.3 76.6 - - - +
41A ASP* 1.3 56.7 + - - +
43A PHE* 3.6 12.4 + - - +
44A LYS* 3.0 28.6 + - - +
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Residues in contact with ASP 41 (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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37A ALA 3.5 9.0 + - - +
38A VAL 3.0 11.1 + - - +
39A PHE 2.9 1.0 - - - -
40A ASP* 1.3 76.9 - - - +
42A LEU* 1.3 62.7 + - - +
44A LYS* 3.9 6.4 - - - +
45A HIS* 3.0 30.9 + - - +
114A GLY 5.0 1.0 - - - +
118A ALA* 3.5 20.0 - - + +
121A ARG* 2.7 47.1 + - - +
122A VAL* 4.6 6.1 - - + +
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Residues in contact with LEU 42 (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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38A VAL 3.1 6.0 + - - +
39A PHE* 2.6 47.7 + - + +
41A ASP* 1.3 75.3 - - - +
43A PHE* 1.3 56.2 + - + +
45A HIS 3.3 0.7 + - - -
46A TYR* 2.7 52.2 + - + +
49A SER* 3.9 11.2 - - - +
111A TYR* 3.9 20.9 - - - +
114A GLY 3.9 5.8 - - - -
115A ILE* 3.9 30.1 - - + +
118A ALA* 4.8 2.0 - - + -
160A HEM 4.1 21.8 - - + -
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Residues in contact with PHE 43 (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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39A PHE* 2.8 44.5 + + + +
40A ASP* 4.0 12.6 - - - +
42A LEU* 1.3 83.8 - - + +
44A LYS* 1.3 63.0 + - - +
45A HIS 3.0 2.0 - - - -
46A TYR 4.2 3.6 - - - -
47A PRO* 3.1 27.1 - - - +
49A SER* 3.4 21.8 - - - -
50A LYS* 3.8 49.4 - - + +
53A PHE* 3.9 27.6 - + - -
58A ILE* 5.1 11.4 - - + -
66A PHE* 5.2 8.1 - + - -
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Residues in contact with LYS 44 (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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40A ASP 3.0 19.4 + - - +
41A ASP* 4.2 3.6 - - - +
42A LEU 3.3 0.4 - - - -
43A PHE* 1.3 76.5 - - - +
45A HIS* 1.3 78.9 + - + +
47A PRO* 4.5 3.4 - - - +
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Residues in contact with HIS 45 (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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41A ASP* 3.0 27.5 + - - +
42A LEU 3.3 1.4 + - - -
43A PHE 3.0 0.2 - - - -
44A LYS* 1.3 101.4 - - + +
46A TYR* 1.3 84.8 + + + +
47A PRO* 3.3 11.6 - - - +
117A GLU* 5.1 2.7 - - - -
121A ARG* 3.2 34.3 + - - +
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Residues in contact with TYR 46 (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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42A LEU* 2.7 33.7 + - + +
43A PHE* 3.7 0.4 - - - -
45A HIS* 1.3 94.5 - + + +
47A PRO* 1.3 53.5 - - - +
48A THR* 2.8 17.8 + - - +
49A SER* 2.7 29.5 + - - -
110A GLU* 3.6 41.5 - - + -
111A TYR* 4.1 23.6 - + + -
113A ARG* 3.6 16.4 + - - -
114A GLY* 3.8 17.5 - - - -
117A GLU* 2.9 33.7 + - - -
121A ARG* 5.9 0.2 - - - -
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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
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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