Contacts of the helix formed by residues 57 - 66 (chain A) in PDB entry 1ORZ
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 PHE 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A SER* 4.7 0.2 + - - -
56A LEU* 1.3 74.8 - - - +
58A PRO* 1.3 67.1 - - + +
59A THR* 2.9 47.6 - - + -
60A ARG* 2.7 45.8 + - + +
61A SER 3.8 1.6 + - - -
168A TYR* 2.9 39.3 - + - -
178A PHE* 5.5 2.2 - + - -
180A ILE* 2.9 37.8 - - + +
181A GLU* 5.1 2.0 + - - -
64B ARG* 5.8 4.9 - - - +
121B TYR* 3.5 52.0 - + - +
161B LEU* 4.4 2.9 - - + -
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Residues in contact with PRO 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ALA* 3.6 26.7 - - + +
37A LEU* 4.5 7.4 - - + -
56A LEU 3.5 1.1 - - - +
57A PHE* 1.3 100.2 - - + +
59A THR* 1.3 61.3 + - - +
60A ARG 3.3 0.3 + - - -
61A SER* 3.2 22.3 + - - +
164A LEU* 3.6 7.7 - - - +
168A TYR* 3.9 25.6 - - + -
178A PHE* 3.0 49.6 - - + -
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Residues in contact with THR 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A PHE* 2.9 32.1 - - + -
58A PRO* 1.3 75.9 - - - +
60A ARG* 1.3 75.2 + - - +
61A SER 3.3 0.2 - - - -
64A VAL* 3.6 13.3 - - - +
164A LEU* 3.2 30.1 - - + +
165A HIS* 3.8 33.2 + - + +
168A TYR* 4.2 15.3 - - + -
72B CYS 4.6 4.0 - - - +
160B ILE 5.0 0.2 - - - -
161B LEU* 3.9 12.0 - - + +
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Residues in contact with ARG 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A LEU* 3.5 23.1 - - + -
57A PHE* 2.7 32.8 + - + +
59A THR* 1.3 86.4 + - - +
61A SER* 1.3 67.3 + - - +
62A HIS* 4.5 0.3 - - - -
64A VAL* 4.0 5.1 - - - +
64B ARG* 5.2 12.1 - - - +
66B SER* 3.2 18.0 + - - +
67B CYS* 5.5 0.7 - - - +
72B CYS* 2.7 39.5 + - - +
73B GLY 3.3 21.4 + - - -
74B SER* 3.2 30.6 + - - +
117B LEU* 5.2 6.1 - - - +
121B TYR* 3.7 17.9 + - - -
160B ILE 3.3 17.6 + - - -
161B LEU* 3.3 16.6 + - - +
162B CYS* 4.7 1.6 + - - +
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Residues in contact with SER 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ALA* 4.5 5.6 - - - -
33A GLY* 3.6 26.5 - - - -
54A SER* 5.8 0.7 - - - -
56A LEU* 5.2 3.1 - - - +
57A PHE 3.8 2.2 + - - -
58A PRO 3.2 11.2 + - - -
59A THR 3.3 0.6 - - - -
60A ARG* 1.3 87.2 - - - +
62A HIS* 1.3 56.0 + - - +
63A THR* 3.1 21.2 + - - -
64A VAL* 2.9 26.7 + - - +
164A LEU* 3.2 8.8 - - - +
234A THR* 5.6 4.0 - - - -
66B SER* 5.2 0.2 - - - -
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Residues in contact with HIS 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A ARG 4.5 0.7 - - - -
61A SER* 1.3 72.6 - - - +
63A THR* 1.3 68.9 + - + +
64A VAL* 4.8 0.9 - - - -
65A ALA* 3.0 28.9 + - + +
66A ALA* 4.1 2.5 + - + -
230A THR* 4.0 9.6 + - - -
231A SER* 3.1 37.5 + - - -
232A ALA* 3.4 23.1 + - - +
234A THR* 4.9 10.1 - - + +
235A CYS* 3.5 21.0 - - - -
370A HIS* 5.4 6.1 + - - -
405A GLU* 5.6 6.0 + - - -
67B CYS* 6.3 2.0 - - - -
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Residues in contact with THR 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A GLY* 4.0 6.3 - - - -
34A GLY* 3.1 34.9 + - - +
61A SER* 3.1 4.4 + - - -
62A HIS* 1.3 80.8 - - + +
64A VAL* 1.3 63.0 + - - +
65A ALA 3.0 1.0 + - - -
66A ALA* 3.0 17.1 + - - +
160A GLY* 3.4 15.0 - - - -
163A LEU* 5.5 3.1 - - - -
164A LEU* 2.9 31.6 - - - +
422A LEU* 5.1 7.0 - - + -
425A LEU* 4.0 16.4 - - + -
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Residues in contact with VAL 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A THR 3.6 12.8 - - - +
60A ARG 4.0 5.8 - - - +
61A SER 2.9 16.9 + - - +
62A HIS* 4.2 1.8 - - - +
63A THR* 1.3 81.0 + - - +
65A ALA* 1.3 63.4 + - + +
66A ALA 4.3 0.7 - - - +
158A ARG* 5.9 0.3 - - - -
161A HIS* 3.2 58.7 + - + +
164A LEU* 3.3 18.2 - - + -
165A HIS* 4.4 3.4 - - - +
67B CYS* 5.0 3.8 - - + -
71B ILE* 3.5 28.3 - - + +
72B CYS* 4.5 8.7 - - + +
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Residues in contact with ALA 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A HIS* 3.0 28.7 + - + +
63A THR 3.0 0.2 + - - -
64A VAL* 1.3 82.6 - - + +
66A ALA* 1.4 62.8 + - - +
67A GLN* 3.1 10.9 + - - +
157A ASP 5.2 0.2 - - - +
230A THR 6.0 0.2 - - - +
269A LEU* 5.9 1.3 - - - +
67B CYS* 5.1 6.3 - - + -
69B GLU* 3.6 27.6 - - - +
71B ILE* 4.1 13.6 - - + +
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Residues in contact with ALA 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A HIS* 4.1 2.5 + - + -
63A THR* 3.0 17.1 + - - +
64A VAL 4.3 0.2 - - - +
65A ALA* 1.4 75.4 - - - +
67A GLN* 1.4 58.3 + - - +
68A GLY 5.4 0.7 - - - +
157A ASP 4.0 0.9 - - - +
158A ARG 4.0 1.9 - - - -
159A THR* 3.8 2.1 + - - -
160A GLY* 2.6 36.5 + - - -
161A HIS 4.2 0.3 + - - -
269A LEU* 6.0 3.1 - - - -
422A LEU* 4.0 27.1 - - + -
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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