Contacts of the helix formed by residues 72 - 78 (chain A) in PDB entry 5T5I
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 ARG 72 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A GLY 3.3 18.4 + - - +
69A ARG* 3.8 8.5 - - - +
70A MET 3.3 1.8 - - - -
71A TYR* 1.4 95.3 - - + +
73A PRO* 1.3 65.8 - - - +
74A GLU* 2.9 35.3 + - - +
75A ASP* 3.1 33.1 + - + +
76A SER* 3.5 6.8 + - - -
93A SER* 3.9 5.7 + - - -
94A VAL* 5.2 1.3 - - + -
313A GLU* 2.9 29.9 + - - +
314A THR* 3.1 21.2 + - - +
315A THR* 2.9 38.9 + - - -
334A LYS* 4.2 1.6 - - - +
350A PRO* 3.9 15.6 - - - +
144C TRP* 3.6 12.3 - - - -
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Residues in contact with PRO 73 (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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69A ARG 5.0 1.6 - - - +
70A MET 3.8 1.5 - - - +
71A TYR 3.4 9.0 - - - +
72A ARG* 1.3 88.9 - - - +
74A GLU* 1.4 59.1 + - - +
76A SER* 3.2 6.4 + - - +
77A LYS* 2.9 26.0 + - - +
127B GLN* 3.7 30.3 - - + +
305B GLY 5.1 0.4 - - - +
306B TYR* 3.5 28.2 + - + -
319B TYR* 3.9 18.2 - - + -
140C TYR* 3.9 5.1 - - + -
141C ARG* 3.3 27.8 - - + +
142C GLY* 3.9 0.4 - - - -
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Residues in contact with GLU 74 (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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72A ARG* 2.9 34.8 + - - +
73A PRO* 1.4 83.0 - - - +
75A ASP* 1.4 66.0 + - - +
77A LYS* 3.5 3.5 + - - +
78A ARG* 3.3 23.4 + - - +
313A GLU* 5.4 0.2 - - - +
334A LYS* 2.9 34.9 + - - -
140C TYR* 4.2 11.7 - - + -
141C ARG 3.8 4.9 + - - +
142C GLY 3.4 8.5 - - - -
143C ASP* 3.9 37.0 - - + +
144C TRP* 3.7 4.2 - - + -
145C ARG* 4.8 3.8 - - - +
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Residues in contact with ASP 75 (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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72A ARG* 3.1 38.6 + - + +
74A GLU* 1.4 81.6 - - - +
76A SER* 1.3 60.7 + - - +
78A ARG* 3.8 13.3 + - - +
79A ASP 3.8 7.6 + - - -
91A GLY* 3.6 5.2 - - - -
92A PHE* 3.1 32.1 + - - +
93A SER* 3.0 34.7 + - - -
94A VAL* 3.0 29.8 + - - +
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Residues in contact with SER 76 (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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69A ARG 5.2 0.3 + - - -
72A ARG 3.5 5.2 + - - -
73A PRO 3.2 6.1 + - - -
75A ASP* 1.3 75.7 - - - +
77A LYS* 1.4 66.2 + - - +
78A ARG 3.1 2.0 - - - -
79A ASP 3.0 22.3 + - - +
80A ALA* 3.4 7.3 + - - +
90A SER* 2.7 31.5 + - - -
91A GLY* 3.7 9.7 + - - +
94A VAL 5.5 0.3 + - - -
305B GLY* 3.5 15.9 + - - -
306B TYR* 3.3 24.5 - - - -
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Residues in contact with LYS 77 (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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73A PRO 2.9 15.3 + - - +
74A GLU* 3.5 6.0 + - - +
76A SER* 1.4 75.0 - - - +
78A ARG* 1.3 60.9 + - - +
79A ASP 3.4 1.0 + - - -
80A ALA* 4.7 6.4 + - - +
306B TYR* 3.2 10.2 + - - +
78C ARG* 6.1 0.8 - - - +
119C GLN* 4.9 5.9 + - - -
120C ASP* 3.9 16.6 + - - -
140C TYR* 3.6 50.7 - - + +
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Residues in contact with ARG 78 (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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74A GLU 3.3 16.4 + - - +
75A ASP* 3.8 10.7 + - - +
76A SER 3.1 0.8 - - - -
77A LYS* 1.3 77.4 - - - +
79A ASP* 1.3 57.9 + - + +
92A PHE* 3.2 60.4 - - + +
312A ASP* 4.9 5.1 + - - -
313A GLU* 3.3 41.1 + - - +
394A ARG* 5.9 0.2 - - - +
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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