Contacts of the helix formed by residues 56 - 65 (chain B) in PDB entry 6UPR
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 56 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B GLY 3.2 4.0 + - - -
55B ILE* 1.3 75.5 - - - +
57B LYS* 1.3 56.3 + - - -
59B THR* 3.5 1.6 + - - -
60B LEU* 3.0 31.4 + - - +
156B PHE* 4.2 4.6 - - - -
401B GTP 2.5 52.2 + - - -
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Residues in contact with LYS 57 (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 CYS* 4.1 17.2 + - + +
51B GLY* 3.5 35.0 + - - +
52B GLU 4.1 6.4 + - - -
53B THR* 5.1 1.2 - - - +
55B ILE* 3.6 13.9 - - + -
56B GLY* 1.3 68.1 - - - +
58B SER* 1.3 64.0 + - - +
60B LEU* 3.3 3.6 + - - +
61B MET* 3.1 28.9 + - - +
103B ASP* 2.6 36.9 + - - +
104B ALA 3.4 14.5 + - - -
105B VAL* 5.0 1.8 - - - +
106B GLY 5.3 2.0 - - - +
107B PHE* 5.3 0.4 - - - +
156B PHE* 3.7 25.4 - - + -
401B GTP 2.3 44.7 + - - +
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Residues in contact with SER 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LYS* 1.3 72.9 - - - +
59B THR* 1.3 64.7 + - - +
61B MET* 3.4 6.8 + - - +
62B ASN* 3.1 32.4 + - - +
71B THR* 3.2 30.0 + - - +
84B ARG* 5.0 1.4 + - - -
103B ASP* 5.3 0.3 + - - -
401B GTP 2.8 19.8 + - - -
402B MG 2.0 30.0 - - - -
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Residues in contact with THR 59 (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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56B GLY 3.7 4.7 - - - -
58B SER* 1.3 76.4 - - - +
60B LEU* 1.3 53.7 + - - +
62B ASN* 3.2 9.9 + - - +
63B THR* 2.7 34.9 + - - +
241B GLY* 3.4 33.2 - - - +
242B SER* 3.6 9.9 - - - +
243B THR* 4.8 4.5 - - + +
401B GTP 2.9 46.1 + - + -
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Residues in contact with LEU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B GLY 3.0 18.3 + - - +
57B LYS 3.3 3.1 + - - +
59B THR* 1.3 76.7 - - - +
61B MET* 1.3 62.2 + - + +
63B THR* 3.2 3.0 + - - -
64B LEU* 2.9 36.9 + - + +
156B PHE* 3.5 28.9 - - + -
184B ILE* 3.7 17.7 - - + -
239B VAL* 3.8 24.7 - - + -
240B VAL 4.6 0.2 - - - +
241B GLY* 4.5 16.5 - - - +
273B PHE* 4.0 27.4 - - + -
276B LEU* 4.0 11.4 - - + -
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Residues in contact with MET 61 (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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47B ILE* 4.4 10.3 - - + -
49B CYS* 3.7 27.8 - - - -
57B LYS 3.1 16.8 + - - +
58B SER* 3.6 9.6 - - - +
60B LEU* 1.3 79.6 - - + +
62B ASN* 1.3 65.2 + - - +
64B LEU* 3.2 24.8 + - + -
65B PHE* 3.3 28.3 + - - -
69B PHE* 3.7 4.6 - - + -
101B ILE* 4.2 37.0 - - + -
154B LEU* 3.6 31.0 - - + -
156B PHE* 4.4 6.7 - - + -
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Residues in contact with ASN 62 (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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58B SER* 3.1 20.6 + - - +
59B THR* 3.6 9.0 - - - +
61B MET* 1.3 75.7 - - - +
63B THR* 1.3 57.1 + - - +
66B ASN* 3.2 6.4 + - - -
67B THR 2.9 40.8 + - - +
68B THR* 3.7 25.6 + - - +
69B PHE* 3.3 33.2 + - - +
71B THR* 5.2 1.8 - - - +
243B THR* 3.8 19.3 + - + +
254B ARG* 4.1 0.3 + - - -
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Residues in contact with THR 63 (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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59B THR* 2.7 21.7 + - - +
60B LEU* 3.7 7.6 - - - -
61B MET 3.2 0.2 - - - -
62B ASN* 1.3 76.1 - - - +
64B LEU* 1.3 65.4 + - - +
241B GLY* 3.7 3.4 - - - -
242B SER 3.1 34.4 + - - +
243B THR* 4.2 3.3 - - - +
254B ARG* 2.3 39.9 + - - +
265B VAL* 3.6 23.8 - - + -
273B PHE* 3.2 26.4 - - + -
277B ARG* 5.1 0.3 + - - -
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Residues in contact with LEU 64 (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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47B ILE* 6.0 0.4 - - + -
60B LEU* 2.9 29.9 + - + +
61B MET* 3.2 30.0 + - + +
63B THR* 1.3 79.7 - - - +
65B PHE* 1.3 64.4 + - + +
66B ASN* 3.6 1.4 + - - +
92B GLU* 4.0 4.9 - - - +
154B LEU* 4.3 5.8 - - + -
273B PHE* 3.5 23.1 - - + -
276B LEU* 4.2 18.2 - - + +
277B ARG* 3.7 49.9 + - + +
279B MET* 5.3 8.3 - - + -
280B LEU* 3.9 22.9 - - + +
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Residues in contact with PHE 65 (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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47B ILE* 4.0 12.8 - - + -
61B MET* 3.3 21.8 + - - +
64B LEU* 1.3 82.0 - - + +
66B ASN* 1.3 71.0 + - - +
67B THR* 3.3 23.2 + - + +
69B PHE* 3.7 15.3 - + + -
90B LEU* 3.9 14.0 - - + +
92B GLU* 3.7 31.4 - - + +
97B LEU* 4.3 17.9 - - + -
99B LEU* 3.5 35.7 - - + -
101B ILE* 4.7 4.5 - - + -
280B LEU* 3.8 34.3 - - + -
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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