Contacts of the helix formed by residues 45 - 58 (chain B) in PDB entry 2GTP
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 GLY 45 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43B GLU 3.4 0.8 - - - -
44B SER* 1.3 79.4 - - - +
46B LYS* 1.3 66.3 + - - +
48B THR* 3.2 3.5 + - - -
49B ILE* 3.1 26.2 + - - +
224B CYS* 4.5 5.4 - - - -
269B ASN* 3.9 10.3 - - - -
326B ALA* 4.3 0.7 - - - +
403B GDP 2.9 32.7 + - - -
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Residues in contact with LYS 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B LEU* 3.2 36.2 - - + +
39B LEU* 3.6 34.1 - - - +
40B GLY 3.2 9.1 + - - +
41B ALA 2.7 26.5 + - - -
44B SER* 3.1 6.8 + - - +
45B GLY* 1.3 76.1 - - - +
47B SER* 1.3 63.4 + - - +
49B ILE* 3.2 3.0 + - - +
50B VAL* 3.1 16.3 + - - +
200B ASP* 3.4 12.8 - - - +
201B VAL* 3.1 26.9 - - + +
202B GLY 4.4 0.4 - - - -
203B GLY 4.0 2.2 - - - +
224B CYS* 4.2 11.4 - - - -
355B ALF 2.9 16.7 - - - -
403B GDP 2.6 25.6 + - - +
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Residues in contact with SER 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LYS* 1.3 70.8 - - - +
48B THR* 1.3 59.4 + - - +
50B VAL* 3.2 6.4 + - - +
51B LYS* 2.9 44.1 + - - +
179B VAL 5.3 2.7 - - - -
181B THR* 3.0 8.7 + - - +
200B ASP* 2.6 25.2 + - - -
402B MG 2.5 24.1 - - - -
403B GDP 2.8 19.6 + - - -
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Residues in contact with THR 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B GLY 3.2 6.9 + - - -
47B SER* 1.3 75.1 - - - +
49B ILE* 1.3 64.9 + - - +
51B LYS* 3.2 12.2 + - - +
52B GLN* 2.9 26.0 + - - +
175B LEU* 3.8 24.3 + - + +
177B THR 5.2 0.7 + - - -
326B ALA* 3.4 31.6 - - + +
327B THR* 3.9 10.8 - - + -
403B GDP 2.6 47.3 + - + -
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Residues in contact with ILE 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LEU* 4.0 18.8 - - + -
45B GLY 3.1 14.2 + - - +
46B LYS* 3.6 7.9 - - - +
48B THR* 1.3 75.5 - - - +
50B VAL* 1.3 63.8 + - - +
52B GLN* 3.1 6.4 + - - +
53B MET* 2.9 41.6 + - + +
198B MET* 4.6 2.7 - - + -
222B ILE* 5.1 4.3 - - + -
224B CYS* 4.8 7.0 - - - -
267B PHE* 3.9 35.7 - - + -
269B ASN* 5.5 2.0 - - - +
324B THR* 5.6 1.1 - - - -
326B ALA* 3.9 14.4 - - + -
332B VAL* 3.7 31.9 - - + -
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Residues in contact with VAL 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LEU* 3.3 26.5 - - + -
46B LYS 3.1 11.3 + - - +
47B SER* 3.2 10.5 + - - +
49B ILE* 1.3 76.5 - - - +
51B LYS* 1.3 63.9 + - + +
53B MET* 3.1 18.9 + - - +
54B LYS* 3.2 11.1 + - - +
187B THR* 4.3 21.8 - - + +
198B MET* 4.2 11.4 - - + -
200B ASP* 3.6 29.8 - - + +
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Residues in contact with LYS 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B SER* 2.9 27.7 + - - +
48B THR* 3.2 13.0 + - - +
50B VAL* 1.3 77.8 - - + +
52B GLN* 1.3 59.8 + - - +
54B LYS* 3.1 16.1 + - - +
55B ILE* 3.1 18.2 + - - +
61B TYR* 3.4 26.8 - - + +
69B TYR* 4.2 16.0 - - - +
174B VAL* 4.0 20.1 + - + +
175B LEU* 3.8 19.5 - - + +
177B THR* 3.0 35.8 + - - -
179B VAL* 5.3 10.7 - - - +
403B GDP 5.9 0.8 + - - -
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Residues in contact with GLN 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B THR 2.9 16.0 + - - +
49B ILE* 3.1 7.8 + - - +
51B LYS* 1.3 77.3 - - - +
53B MET* 1.3 57.4 + - - +
55B ILE* 3.2 9.9 + - - +
56B ILE* 2.9 38.3 + - + +
175B LEU* 3.6 12.9 - - + +
326B ALA 2.7 30.1 + - - +
327B THR 3.3 11.5 + - - -
328B ASP 3.5 1.4 - - - -
329B THR* 2.6 55.7 + - - +
332B VAL* 3.7 25.1 - - + -
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Residues in contact with MET 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ILE* 2.9 37.4 + - + +
50B VAL* 3.1 7.8 + - + +
52B GLN* 1.3 71.9 - - - +
54B LYS* 1.3 65.4 + - - +
56B ILE* 5.0 1.6 - - + -
57B HIS* 3.0 53.8 + - + +
58B GLU* 3.6 2.4 + - - +
187B THR* 6.0 1.8 - - + -
189B PHE* 3.9 22.2 - - + -
198B MET* 3.4 28.0 - - + -
267B PHE* 6.0 0.4 - - + -
332B VAL* 3.8 23.3 - - + -
336B PHE* 3.6 38.1 - - + -
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Residues in contact with LYS 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B VAL 3.2 8.8 + - - +
51B LYS* 3.1 13.7 + - - +
53B MET* 1.3 74.4 - - - +
55B ILE* 1.3 59.9 + - - +
58B GLU* 2.9 46.0 + - + +
60B GLY* 3.6 6.8 + - - +
61B TYR* 4.8 14.4 - - + +
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Residues in contact with ILE 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B LYS 3.1 14.1 + - - +
52B GLN* 3.2 25.1 + - - +
54B LYS* 1.3 77.2 - - - +
56B ILE* 1.3 63.0 + - - +
59B ALA* 3.4 5.5 + - - -
60B GLY* 3.1 24.5 + - - +
61B TYR* 3.9 25.4 - - + -
171B GLN* 3.5 35.7 - - + +
175B LEU* 3.9 24.9 - - + -
329B THR* 4.1 19.3 - - + +
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Residues in contact with ILE 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B GLN* 2.9 27.4 + - + +
53B MET* 5.0 4.7 - - + -
55B ILE* 1.3 75.9 - - + +
57B HIS* 1.3 84.7 + - + +
59B ALA* 4.6 1.6 + - - -
191B PHE* 6.0 1.6 - - + -
329B THR* 4.1 22.2 - - + +
332B VAL* 4.1 16.4 - - + +
333B GLN* 3.7 59.2 - - + +
336B PHE* 5.6 0.9 - - + -
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Residues in contact with HIS 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B MET* 3.0 35.1 + - + +
56B ILE* 1.3 101.3 - - + +
58B GLU* 1.3 68.6 + - - +
59B ALA 3.5 1.3 - - - -
189B PHE* 3.8 27.3 - + + -
190B THR 4.3 9.4 - - - +
191B PHE* 3.5 43.8 - + + -
336B PHE* 3.5 32.3 - + + -
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Residues in contact with GLU 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B MET 3.6 3.5 + - - +
54B LYS* 2.9 23.9 + - + +
57B HIS* 1.3 85.1 - - + +
59B ALA* 1.3 68.5 + - - +
60B GLY 4.4 2.4 - - - +
188B HIS 4.2 6.2 - - - +
189B PHE* 3.4 36.2 - - + +
190B THR* 3.9 6.4 + - - +
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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