Contacts of the strand formed by residues 33 - 40 (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 GLU 33 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32B ARG* 1.3 80.0 - - - +
34B VAL* 1.3 65.9 + - - +
35B LYS 4.2 0.8 + - - -
195B HIS* 3.3 16.6 - - + +
197B LYS* 3.4 33.9 + - + +
219B THR* 4.5 4.9 + - - +
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Residues in contact with VAL 34 (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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33B GLU* 1.3 80.9 - - - +
35B LYS* 1.3 66.0 + - - +
36B LEU* 3.5 3.3 + - + +
194B LEU* 4.0 38.1 - - + -
195B HIS 2.8 10.4 + - - +
196B PHE* 3.3 33.4 - - + +
197B LYS* 2.8 27.5 + - - -
219B THR* 4.0 17.3 - - + -
220B ALA* 5.1 0.7 - - + -
343B ILE* 4.2 24.9 - - + -
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Residues in contact with LYS 35 (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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33B GLU* 4.2 1.0 - - - +
34B VAL* 1.3 71.4 - - - +
36B LEU* 1.3 60.5 + - - +
37B LEU* 4.3 1.6 - - + -
197B LYS* 3.5 7.6 - - + -
199B PHE* 3.7 37.5 - - + -
213B HIS 5.2 1.0 + - - -
214B CYS* 3.2 31.8 + - - +
216B GLU* 2.8 32.6 + - - +
217B GLY 3.7 19.3 - - - +
218B VAL* 3.8 9.1 - - + +
219B THR* 3.0 27.9 + - - +
220B ALA* 3.1 10.6 + - - +
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Residues in contact with LEU 36 (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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34B VAL* 3.5 2.2 + - + -
35B LYS* 1.3 73.8 - - - +
37B LEU* 1.3 66.6 + - - +
38B LEU* 3.8 8.5 + - + -
196B PHE* 4.1 25.1 - - + -
197B LYS 3.0 9.9 + - - +
198B MET* 3.3 37.3 - - + -
199B PHE 2.9 26.9 + - - -
220B ALA* 3.4 28.5 - - + +
222B ILE* 3.8 27.6 - - + +
336B PHE* 4.0 20.0 - - + -
339B VAL* 5.6 1.1 - - + -
343B ILE* 5.3 4.9 - - + -
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Residues in contact with LEU 37 (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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35B LYS* 4.3 3.1 - - + -
36B LEU* 1.3 81.9 - - - +
38B LEU* 1.3 62.9 + - - +
39B LEU* 3.7 17.7 + - + -
199B PHE* 3.6 24.2 - - + +
214B CYS* 3.7 37.5 - - - +
215B PHE* 4.2 16.2 - - + -
218B VAL* 3.5 34.1 - - + -
220B ALA 3.0 7.5 + - - -
221B ILE* 3.4 10.5 - - + +
222B ILE 2.9 29.6 + - - +
259B PHE* 4.2 9.9 - - + -
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Residues in contact with LEU 38 (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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36B LEU* 3.8 13.0 - - + -
37B LEU* 1.3 76.4 - - - +
39B LEU* 1.3 61.0 + - - +
46B LYS* 3.2 44.4 - - + +
49B ILE* 4.0 15.3 - - + -
50B VAL* 3.3 23.1 - - + -
198B MET* 3.4 34.1 - - + -
199B PHE 2.9 14.7 + - - +
200B ASP* 4.3 3.4 - - + +
201B VAL* 3.3 26.0 + - - +
222B ILE* 3.5 17.9 - - + +
224B CYS* 5.5 1.3 - - - -
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Residues in contact with LEU 39 (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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37B LEU* 4.0 27.8 - - + -
38B LEU* 1.3 77.9 - - - +
40B GLY* 1.3 53.6 + - - +
46B LYS* 3.6 8.0 - - - +
201B VAL* 3.5 28.3 - - + -
211B TRP* 3.7 22.9 - - + -
214B CYS* 5.1 0.7 - - - -
215B PHE* 4.5 6.3 - - + -
221B ILE* 3.8 26.9 - - + -
222B ILE 3.0 5.7 + - - +
223B PHE* 3.3 13.2 - - + -
224B CYS* 2.7 35.7 + - - +
253B ILE* 4.0 31.6 - - + -
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Residues in contact with GLY 40 (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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39B LEU* 1.3 78.7 - - - +
41B ALA* 1.3 66.6 + - - +
44B SER* 3.7 4.3 - - - -
46B LYS* 3.2 9.4 + - - +
203B GLY* 3.4 11.8 - - - -
211B TRP* 3.7 10.0 - - - -
223B PHE* 4.1 14.5 - - - -
224B CYS 3.4 15.7 - - - -
249B LEU* 3.9 6.5 - - - -
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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