Contacts of the helix formed by residues 42 - 59 (chain N) 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 ASP 42 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38M LEU* 3.7 12.5 - - - +
39M THR* 2.7 37.2 + - - +
39N GLU 4.5 10.4 - - - +
40N LYS 3.4 5.4 + - - +
41N ILE* 1.3 74.5 - - - +
43N PRO* 1.3 60.4 - - - +
44N GLU 3.3 0.3 + - - -
45N HIS* 2.9 38.5 + - + +
46N PHE* 3.1 25.5 + - - +
38O ARG* 3.6 4.0 - - - +
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Residues in contact with PRO 43 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39M THR* 4.2 0.9 - - - +
40M HIS 3.9 16.8 - - - +
41M ASP* 4.3 19.1 - - - +
42M VAL* 4.7 13.5 - - + -
41N ILE* 3.5 5.1 - - + +
42N ASP* 1.3 82.3 - - - +
44N GLU* 1.3 62.7 + - - +
45N HIS 2.6 15.6 + - - -
46N PHE* 2.9 8.1 + - + +
47N VAL* 2.8 26.7 + - - +
38O ARG* 3.2 26.7 - - + +
43O ARG* 5.9 6.1 - - - -
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Residues in contact with GLU 44 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39M THR* 3.6 38.3 - - + +
40M HIS* 3.9 19.7 + - - +
41M ASP 5.6 0.5 - - - +
42M VAL* 3.7 16.4 - - + +
42N ASP* 3.3 0.6 + - - -
43N PRO* 1.3 79.9 - - - +
45N HIS* 1.3 56.6 + - - +
47N VAL* 3.1 21.5 - - + +
48N SER* 3.7 10.0 - - - -
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Residues in contact with HIS 45 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39M THR* 6.1 0.4 - - + -
42N ASP* 2.9 32.0 + - + +
43N PRO 2.6 5.1 + - - -
44N GLU* 1.3 74.0 - - - +
46N PHE* 1.3 73.2 + - - +
48N SER* 2.9 17.8 + - - -
49N GLU* 3.0 12.5 + - + +
199N ARG 5.3 1.4 + - - +
200N GLY 5.6 2.4 - - - -
201N ASP* 3.0 33.6 + - + -
203N GLU* 5.9 0.9 - - - -
204N ARG* 3.2 28.3 + - - -
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Residues in contact with PHE 46 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47M ILE* 5.8 7.0 - - + -
42N ASP 3.1 15.2 + - - +
43N PRO* 2.9 8.6 + - + +
45N HIS* 1.3 86.5 + - - +
47N VAL* 1.3 71.3 + - + +
49N GLU* 2.7 26.6 + - - +
50N ILE* 3.0 41.8 + - + +
47O ALA* 3.7 41.1 - - + -
48O GLY* 5.0 0.7 - - - -
50O LEU* 4.5 8.5 - - + -
51O ARG* 4.2 35.4 - - + -
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Residues in contact with VAL 47 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42M VAL* 3.9 20.4 - - + -
46M THR* 3.9 26.9 - - + -
47M ILE* 5.2 8.7 - - + -
50M LEU* 4.3 17.4 - - + +
43N PRO 2.8 17.4 + - - +
44N GLU* 3.1 26.0 - - + +
46N PHE* 1.3 85.7 - - + +
48N SER* 1.3 71.7 + - - +
50N ILE* 3.0 6.0 + - - +
51N ASP* 2.8 27.7 + - + +
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Residues in contact with SER 48 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44N GLU 3.7 11.7 - - - -
45N HIS* 2.9 14.0 + - - -
47N VAL* 1.3 83.7 - - - +
49N GLU* 1.3 61.3 + - - +
51N ASP* 3.3 8.6 + - - +
52N ALA* 3.0 25.8 + - - +
200N GLY* 3.3 28.2 + - - -
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Residues in contact with GLU 49 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45N HIS* 3.0 8.9 + - - +
46N PHE* 2.7 31.9 + - - +
48N SER* 1.3 72.2 - - - +
50N ILE* 1.3 60.3 + - + +
52N ALA* 3.9 1.4 - - - +
53N ARG* 2.7 65.1 + - - +
199N ARG* 3.4 33.9 + - + +
204N ARG* 3.5 33.9 + - - +
51O ARG* 4.3 15.9 + - - -
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Residues in contact with ILE 50 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50M LEU* 3.5 22.2 - - + -
54M ILE* 4.0 1.1 - - + -
46N PHE* 3.0 48.0 + - + +
47N VAL* 3.0 6.6 + - - +
49N GLU* 1.3 84.3 - - + +
51N ASP* 1.3 67.2 + - - +
53N ARG* 3.0 11.8 + - + +
54N VAL* 2.7 27.0 + - + +
50O LEU* 3.9 20.9 - - + -
51O ARG* 4.6 16.2 - - + -
54O VAL* 3.9 20.2 - - + -
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Residues in contact with ASP 51 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50M LEU* 4.0 14.2 - - + +
53M ARG* 3.5 28.1 + - - +
47N VAL* 2.8 15.0 + - + +
48N SER* 3.5 13.0 - - - +
50N ILE* 1.3 77.3 - - - +
52N ALA* 1.3 56.0 + - - +
54N VAL* 3.5 1.8 - - - +
55N THR* 2.7 48.0 + - - -
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Residues in contact with ALA 52 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48N SER 3.0 14.0 + - - +
49N GLU 3.9 2.2 - - - +
51N ASP* 1.3 83.9 + - - +
53N ARG* 1.3 64.0 + - - +
55N THR* 3.8 5.8 - - - -
56N LYS* 3.0 25.1 + - - +
198N ASN* 4.7 8.8 + - + +
199N ARG* 4.2 9.4 - - - +
200N GLY* 3.8 23.3 - - - +
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Residues in contact with ARG 53 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49N GLU* 2.7 59.0 + - - +
50N ILE* 3.0 15.2 + - + +
52N ALA* 1.3 73.6 - - - +
54N VAL* 1.3 59.8 + - - +
56N LYS* 3.3 23.3 - - - +
57N ILE* 3.5 11.3 - - - +
198N ASN* 6.2 1.1 - - - +
199N ARG* 4.5 21.7 - - - +
51O ARG* 4.6 16.2 - - - +
54O VAL* 3.7 19.4 - - + +
55O GLU* 4.5 13.1 - - - +
58O GLU* 2.5 52.7 + - - +
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Residues in contact with VAL 54 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50M LEU* 4.9 2.9 - - + -
53M ARG* 4.1 18.6 - - + +
54M ILE* 3.8 25.4 - - + -
57M LEU* 3.8 15.3 - - + -
50N ILE* 2.7 31.9 + - + +
51N ASP 3.5 2.2 - - - +
53N ARG* 1.3 71.4 - - - +
55N THR* 1.3 57.0 + - - +
56N LYS 2.9 1.8 - - - -
57N ILE* 2.6 30.5 + - + +
58N GLU* 2.9 35.2 + - + +
54O VAL* 4.3 11.9 - - + -
57O LEU* 6.1 0.9 - - + -
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Residues in contact with THR 55 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53M ARG* 3.3 8.7 + - - -
51N ASP* 2.7 41.7 + - - -
52N ALA* 3.8 7.4 - - - -
54N VAL* 1.3 72.9 - - - +
56N LYS* 1.3 52.4 + - - +
58N GLU* 3.6 14.8 - - + +
59N GLY* 2.5 34.3 + - - +
60N THR* 4.2 18.7 + - + +
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Residues in contact with LYS 56 (chain N).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52N ALA 3.0 13.1 + - - +
53N ARG* 3.3 18.4 - - - +
54N VAL 2.9 0.2 - - - -
55N THR* 1.3 78.6 - - - +
57N ILE* 1.3 62.3 + - + +
59N GLY* 3.8 7.0 + - - -
198N ASN* 3.9 26.0 - - + +
206N GLU* 4.7 17.3 + - - +
58O GLU* 4.8 13.2 - - - +
59O ASP* 6.0 1.8 - - - -
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Residues in contact with ILE 57 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57M LEU* 4.0 24.2 - - + -
53N ARG 3.5 17.5 - - - +
54N VAL* 2.6 20.3 + - + +
56N LYS* 1.3 74.4 - - + +
58N GLU* 1.3 65.0 + - - +
59N GLY* 3.1 2.1 + - - -
54O VAL* 4.6 6.1 - - + -
57O LEU* 3.8 35.0 - - + +
58O GLU* 4.2 23.1 - - + +
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Residues in contact with GLU 58 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53M ARG* 3.0 51.0 + - - +
57M LEU* 4.1 19.1 - - + +
54N VAL* 2.9 25.4 + - + +
55N THR* 3.6 20.9 + - + +
57N ILE* 1.3 78.4 - - - +
59N GLY* 1.3 68.9 + - - +
61N HIS* 4.6 13.7 + - + +
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Residues in contact with GLY 59 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55N THR* 2.5 21.7 + - - -
56N LYS* 4.1 8.5 - - - -
57N ILE 3.1 2.1 - - - -
58N GLU* 1.3 84.0 - - - +
60N THR* 1.3 70.9 + - - +
61N HIS* 3.3 13.0 + - - -
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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