Contacts of the helix formed by residues 40 - 58 (chain O) 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 40 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36O ASP 2.8 15.3 + - - +
37O ASP* 3.7 18.4 - - - +
38O ARG 3.4 1.0 - - - -
39O LEU* 1.3 73.4 - - - +
41O PRO* 1.3 68.2 - - - +
42O LYS* 3.6 18.2 + - - +
43O ARG* 2.7 56.4 + - + +
44O ILE* 3.2 4.7 + - - +
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Residues in contact with PRO 41 (chain O).
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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39O LEU 2.6 12.0 - - - +
40O ASP* 1.3 87.2 - - - +
42O LYS* 1.3 69.8 + - + +
44O ILE* 2.9 22.5 + - + +
45O ARG* 3.1 32.5 + - - +
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Residues in contact with LYS 42 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40O ASP* 3.1 18.6 + - - +
41O PRO* 1.3 84.2 - - + +
43O ARG* 1.3 60.4 + - - +
45O ARG* 3.6 19.0 - - - +
46O LYS* 3.2 27.4 + - - +
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Residues in contact with ARG 43 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41M ASP* 4.4 22.8 + - - +
43N PRO* 5.9 5.2 - - - -
37O ASP* 3.4 35.9 + - - +
38O ARG* 5.0 10.3 - - - +
40O ASP* 2.7 26.9 + - + +
42O LYS* 1.3 78.9 - - - +
44O ILE* 1.3 65.4 + - + +
46O LYS* 3.4 7.2 + - - +
47O ALA* 2.9 26.5 + - + +
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Residues in contact with ILE 44 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41N ILE* 3.7 43.5 - - + -
38O ARG 4.8 5.6 - - - +
39O LEU 4.2 5.6 - - - +
40O ASP 3.8 11.7 - - - +
41O PRO* 2.9 16.7 + - + +
43O ARG* 1.3 78.4 - - + +
45O ARG* 1.3 56.4 + - - +
47O ALA* 2.8 7.6 + - - +
48O GLY* 2.7 34.7 + - - +
195O TYR* 6.2 3.6 - - + -
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Residues in contact with ARG 45 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41O PRO* 3.1 27.2 + - - +
42O LYS* 3.6 24.4 - - - +
44O ILE* 1.3 81.2 - - + +
46O LYS* 1.3 68.0 + - + +
48O GLY* 3.0 1.2 + - - +
49O SER* 2.5 39.2 + - - -
195O TYR* 3.2 42.3 + - + +
196O ASN* 5.0 12.0 + - - +
197O PHE* 5.9 1.2 - - - -
198O ASP* 6.0 2.0 - - - -
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Residues in contact with LYS 46 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51M LYS* 4.6 22.8 - - - +
42O LYS 3.2 18.6 + - - +
43O ARG* 3.4 7.2 + - + +
44O ILE 3.2 0.4 - - - -
45O ARG* 1.3 85.0 - - + +
47O ALA* 1.3 61.5 + - - +
49O SER* 3.5 7.7 - - - -
50O LEU* 3.4 16.3 + - - +
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Residues in contact with ALA 47 (chain O).
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* 6.1 4.3 - - + -
46N PHE* 3.7 29.4 - - + -
43O ARG* 2.9 20.3 + - + +
44O ILE* 2.8 5.6 + - - +
46O LYS* 1.3 72.3 - - - +
48O GLY* 1.3 69.2 + - - +
49O SER 3.1 1.3 - - - -
50O LEU* 2.8 20.1 + - - +
51O ARG 3.0 9.4 + - - -
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Residues in contact with GLY 48 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46N PHE* 5.0 2.0 - - - -
44O ILE* 2.7 19.5 + - - -
45O ARG 3.5 2.5 - - - -
47O ALA* 1.3 71.8 - - - +
49O SER* 1.3 61.6 + - - +
51O ARG* 2.9 30.5 + - - +
52O HIS 3.0 10.2 + - - -
195O TYR* 3.2 28.4 - - - -
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Residues in contact with SER 49 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45O ARG 2.5 21.9 + - - -
46O LYS* 3.5 10.8 - - - -
48O GLY* 1.3 72.1 - - - +
50O LEU* 1.3 63.0 + - - +
52O HIS* 3.1 19.6 + - - +
53O ARG* 3.3 10.9 + - - +
193O ASP* 2.8 40.2 + - - +
195O TYR* 3.4 5.2 - - - -
196O ASN* 5.1 6.8 + - - +
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Residues in contact with LEU 50 (chain O).
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* 4.9 13.5 - - + -
50M LEU* 4.6 12.3 - - + -
51M LYS* 4.0 31.4 - - + -
54M ILE* 3.8 26.5 - - + -
46N PHE* 4.5 6.5 - - + -
50N ILE* 3.9 25.8 - - + -
46O LYS 3.4 9.0 + - - +
47O ALA* 2.8 13.8 + - - +
49O SER* 1.3 75.8 - - - +
51O ARG* 1.3 74.0 + - - +
53O ARG* 3.1 27.7 + - - +
54O VAL* 3.3 8.0 + - + +
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Residues in contact with ARG 51 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46N PHE* 4.2 29.0 - - + -
49N GLU* 4.3 11.9 + - - -
50N ILE* 4.6 11.2 - - + -
53N ARG* 4.6 18.3 - - - +
47O ALA 3.0 8.0 + - - +
48O GLY* 2.9 18.5 + - - +
50O LEU* 1.3 82.8 - - - +
52O HIS* 1.3 62.7 + - - +
54O VAL* 2.9 16.7 + - - +
55O GLU* 2.9 36.4 + - + +
195O TYR* 4.0 23.0 + - - -
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Residues in contact with HIS 52 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48O GLY 3.0 9.5 + - - +
49O SER* 3.1 12.5 + - - +
51O ARG* 1.3 75.1 - - - +
53O ARG* 1.3 69.7 - - + +
55O GLU* 2.6 37.9 + - + +
56O GLU* 3.0 37.4 + - + +
174O HIS* 6.1 2.7 - + - -
191O GLU* 5.0 7.9 + - - -
192O PHE 4.5 6.1 + - - -
193O ASP* 3.2 38.6 + - - +
194O GLY* 5.6 0.9 - - - -
195O TYR* 4.9 7.4 - - + -
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Residues in contact with ARG 53 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51M LYS* 4.2 25.2 + - - +
54M ILE* 4.1 13.3 - - + +
55M SER* 3.5 26.7 + - - +
58M GLU* 2.7 47.9 + - - +
49O SER* 3.3 12.3 + - - +
50O LEU* 3.1 21.1 + - - +
52O HIS* 1.3 81.3 - - + +
54O VAL* 1.3 59.7 + - - +
56O GLU* 3.4 18.7 - - - +
57O LEU* 3.4 16.1 - - - +
193O ASP* 5.4 3.8 - - - +
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Residues in contact with VAL 54 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54M ILE* 3.4 37.5 - - + -
50N ILE* 3.9 15.5 - - + -
53N ARG* 3.7 34.3 - - + +
54N VAL* 4.3 10.3 - - + -
57N ILE* 4.6 6.5 - - + -
50O LEU* 3.7 9.4 - - + +
51O ARG* 2.9 10.3 + - - +
52O HIS 2.7 2.6 + - - -
53O ARG* 1.3 71.5 - - - +
55O GLU* 1.3 53.9 + - - +
56O GLU 2.9 4.7 - - - -
57O LEU* 2.7 30.2 + - + +
58O GLU* 3.1 17.3 + - + +
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Residues in contact with GLU 55 (chain O).
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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53N ARG* 4.5 10.5 - - - +
51O ARG* 2.9 41.5 + - + +
52O HIS* 2.6 33.2 + - + +
54O VAL* 1.3 71.5 - - - +
56O GLU* 1.3 60.8 + - - +
57O LEU 3.6 0.2 + - - -
58O GLU* 3.6 26.0 + - - +
59O ASP 4.9 1.4 - - - +
60O PRO* 5.9 0.9 - - - +
61O SER* 5.6 5.9 + - - +
68O GLN* 5.8 4.7 - - - +
195O TYR* 4.8 7.8 + - - -
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Residues in contact with GLU 56 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52O HIS* 3.0 34.9 + - + +
53O ARG* 3.4 15.3 - - - +
54O VAL 2.9 0.6 + - - -
55O GLU* 1.3 80.7 - - - +
57O LEU* 1.3 66.3 + - + +
58O GLU 3.8 4.3 - - - +
191O GLU* 4.1 15.9 - - - +
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Residues in contact with LEU 57 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54M ILE* 4.1 19.1 - - + +
57M LEU* 3.5 39.5 - - + +
58M GLU* 3.9 31.9 - - + -
59M GLU 5.5 0.2 - - - +
54N VAL* 6.1 0.4 - - + -
57N ILE* 3.8 22.0 - - + +
53O ARG 3.4 14.4 - - - +
54O VAL* 2.7 17.4 + - + +
56O GLU* 1.3 75.1 - - + +
58O GLU* 1.3 65.1 + - - +
59O ASP 3.8 0.5 + - - -
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Residues in contact with GLU 58 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53N ARG* 2.5 58.5 + - - +
56N LYS* 4.8 12.3 - - - +
57N ILE* 4.2 14.5 - - + +
54O VAL* 3.1 17.6 + - + +
55O GLU* 3.6 23.0 - - - +
56O GLU 3.4 4.9 - - - +
57O LEU* 1.3 81.4 - - - +
59O ASP* 1.3 73.1 + - - +
60O PRO* 3.5 2.3 - - - +
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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