Contacts of the helix formed by residues 33 - 50 (chain G) in PDB entry 1GOT
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 VAL 33 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B CYS 3.0 25.5 + - - +
26B ALA* 3.6 15.5 - - + -
27B ASP* 3.9 2.9 + - - +
28B ALA 3.5 23.8 - - - +
29B THR* 4.6 1.8 - - - -
30B LEU 5.0 0.2 - - - +
257B ALA* 4.3 7.9 - - + -
259B GLN* 4.0 22.2 - - + +
260B GLU 5.9 0.9 - - - +
261B LEU* 3.9 13.5 - - + -
31G MET 3.6 1.4 + - - -
32G LEU* 1.3 69.2 - - - +
34G SER* 1.3 54.1 + - - +
36G CYS* 2.9 9.4 + - - +
37G CYS* 2.5 55.4 + - - +
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Residues in contact with SER 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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27B ASP* 2.7 34.3 + - - -
28B ALA* 4.2 7.6 - - - +
33B ILE* 3.7 22.9 - - - -
32G LEU* 4.1 4.2 - - - +
33G VAL* 1.3 77.1 - - - +
35G LYS* 1.3 56.0 + - - +
37G CYS* 4.2 1.3 - - - -
38G GLU* 2.7 48.9 + - - +
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Residues in contact with LYS 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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31G MET* 4.1 20.8 - - + +
32G LEU* 3.1 44.8 + - + +
34G SER* 1.3 78.7 + - - +
36G CYS* 1.3 64.2 + - - +
38G GLU* 3.8 7.4 - - - +
39G GLU* 3.0 38.6 + - + +
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Residues in contact with CYS 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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254B ASP* 3.2 39.1 - - + +
256B ARG* 3.9 11.2 + - - +
257B ALA* 3.7 20.4 - - + -
261B LEU* 4.9 3.1 - - + -
31G MET* 3.1 30.3 - - - -
32G LEU 3.0 14.2 + - - -
33G VAL* 2.9 9.8 + - - +
35G LYS* 1.3 79.3 - - - +
37G CYS* 1.3 57.9 + - - +
39G GLU* 3.2 3.3 + - - +
40G PHE* 2.8 28.8 + - - +
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Residues in contact with CYS 37 (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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29B THR 4.1 1.6 - - - -
30B LEU* 3.5 46.0 - - + +
33B ILE* 4.0 15.7 - - + -
261B LEU* 4.0 13.2 - - - +
33G VAL* 2.5 42.4 + - - +
34G SER* 3.7 3.8 - - - +
36G CYS* 1.3 73.3 - - - +
38G GLU* 1.3 52.9 + - - +
40G PHE* 2.9 9.6 + - - +
41G ARG* 2.7 36.2 + - - +
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Residues in contact with GLU 38 (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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33B ILE* 3.7 30.1 - - + +
34G SER* 2.7 34.0 + - - +
35G LYS* 3.8 7.2 - - - +
37G CYS* 1.3 72.1 - - - +
39G GLU* 1.3 60.0 + - + +
41G ARG* 3.4 18.7 + - - +
42G ASP* 2.9 41.5 + - - +
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Residues in contact with GLU 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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237B ASN* 4.6 3.9 + - - -
239B ASN* 5.5 1.5 - - - +
256B ARG* 3.1 31.3 + - - +
31G MET* 4.2 8.7 - - - +
35G LYS* 3.0 30.3 + - - +
36G CYS 3.6 4.0 - - - +
38G GLU* 1.3 74.7 - - + +
40G PHE* 1.3 67.3 + - - +
42G ASP* 4.0 8.2 - - - +
43G TYR* 3.2 20.4 + - - +
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Residues in contact with PHE 40 (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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30B LEU* 3.9 13.7 - - + -
235B PHE* 3.5 50.3 - + - -
237B ASN* 4.9 7.2 - - - +
239B ASN* 6.5 0.2 - - + -
240B ALA* 4.4 11.2 - - + -
252B LEU* 3.6 38.4 - - + -
254B ASP* 5.3 2.7 - - - +
261B LEU* 4.7 10.5 - - + -
278B PHE* 5.0 0.2 - + - -
282B GLY 4.9 2.2 - - - -
299B ALA* 4.6 9.4 - - + -
300B LEU* 3.6 28.0 - - + -
36G CYS 2.8 13.1 + - - +
37G CYS* 3.1 12.3 - - - +
39G GLU* 1.3 76.4 - - - +
41G ARG* 1.3 63.3 + - - +
43G TYR* 3.0 17.3 + - - +
44G VAL* 3.2 19.4 + - + +
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Residues in contact with ARG 41 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ILE* 3.1 34.3 + - + +
34B THR* 3.7 22.9 - - + -
36B ASN* 4.9 4.9 + - - +
37B ILE* 4.1 18.2 - - + +
300B LEU* 3.9 13.7 - - + -
37G CYS 2.7 17.8 + - - +
38G GLU* 3.6 29.1 + - - +
40G PHE* 1.3 73.6 - - - +
42G ASP* 1.3 88.6 + - - +
44G VAL* 3.2 2.6 + - - +
45G GLU* 2.9 43.5 + - + +
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Residues in contact with ASP 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 GLU* 2.9 33.6 + - - +
39G GLU* 4.0 7.8 - - - +
41G ARG* 1.3 104.7 + - - +
43G TYR* 1.3 63.8 + - - +
45G GLU* 4.1 5.2 - - - +
46G GLU* 3.0 40.4 + - + +
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Residues in contact with TYR 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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235B PHE* 3.4 17.0 - + + -
236B PRO* 3.5 33.9 + - + +
237B ASN* 3.8 30.7 - - + +
280B LYS 4.7 2.9 + - - -
281B SER 3.5 19.5 - - - -
39G GLU 3.2 13.2 + - - +
40G PHE* 3.0 11.5 + - - +
42G ASP* 1.3 78.9 - - - +
44G VAL* 1.3 57.5 + - - +
46G GLU* 3.4 2.4 + - - -
47G ARG* 2.7 78.7 + - - +
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Residues in contact with VAL 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B PHE* 3.7 26.2 - - + -
281B SER* 3.7 10.5 - - - +
282B GLY 4.0 6.3 - - - +
283B ARG* 3.4 41.7 - - + +
300B LEU* 3.4 34.3 - - + -
40G PHE* 3.2 16.7 + - + +
41G ARG 3.7 1.3 - - - +
43G TYR* 1.3 74.6 - - - +
45G GLU* 1.3 53.1 + - - +
47G ARG* 2.8 7.5 + - - +
48G SER* 2.7 34.6 + - - -
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Residues in contact with GLU 45 (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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37B ILE* 3.8 35.5 - - + +
283B ARG* 3.4 23.3 + - - -
300B LEU* 3.8 11.0 - - + +
41G ARG* 2.9 29.9 + - + +
42G ASP* 4.1 5.2 - - - +
44G VAL* 1.3 76.5 - - - +
46G GLU* 1.3 62.1 + - + +
47G ARG 3.3 0.5 + - - -
48G SER* 3.6 17.4 + - - -
49G GLY 4.8 2.1 + - - -
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Residues in contact with GLU 46 (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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42G ASP* 3.0 33.6 + - + +
43G TYR* 5.2 0.2 - - - -
44G VAL 3.1 0.4 + - - -
45G GLU* 1.3 77.4 - - - +
47G ARG* 1.3 87.3 + - - +
49G GLY 5.3 0.4 + - - -
50G GLU* 3.6 8.1 - - - +
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Residues in contact with ARG 47 (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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280B LYS* 3.3 15.0 + - + +
281B SER* 3.5 24.0 - - - -
43G TYR* 2.7 98.5 + - + +
44G VAL 2.8 5.9 + - - -
46G GLU* 1.3 107.3 + - - +
48G SER* 1.3 62.2 + - - +
49G GLY 3.0 3.4 - - - +
50G GLU* 2.9 36.8 + - + +
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Residues in contact with SER 48 (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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281B SER* 3.5 19.5 - - - -
283B ARG* 4.0 25.8 + - - -
44G VAL* 2.7 22.2 + - - -
45G GLU* 3.6 21.5 + - - -
46G GLU 4.0 0.2 - - - -
47G ARG* 1.3 72.2 - - - +
49G GLY* 1.3 62.8 + - - +
50G GLU 3.1 1.4 + - - -
51G ASP* 3.2 14.2 + - - +
54G VAL* 3.8 19.2 - - - +
55G LYS* 3.9 1.7 - - - +
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Residues in contact with GLY 49 (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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45G GLU 4.8 2.8 + - - -
46G GLU 5.3 0.4 + - - -
47G ARG* 3.0 2.6 + - - +
48G SER* 1.3 82.0 + - - +
50G GLU* 1.3 57.0 + - - +
51G ASP 3.5 0.2 - - - -
55G LYS* 3.3 27.9 - - - +
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Residues in contact with GLU 50 (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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280B LYS* 3.6 19.3 + - - +
46G GLU 3.6 7.1 - - - +
47G ARG* 3.1 32.5 - - - +
49G GLY* 1.3 77.8 - - - +
51G ASP* 1.3 59.0 + - - +
52G PRO* 3.1 15.8 - - - +
55G LYS* 4.8 1.1 - - - -
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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