Contacts of the helix formed by residues 69 - 78 (chain A) in PDB entry 3REZ
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 LEU 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A SER* 3.9 28.3 - - - -
42A VAL 4.7 0.7 - - - +
63A TRP* 4.0 16.4 - - + -
64A ARG 3.7 20.2 - - - +
65A CYS* 3.7 25.6 - - - -
66A ASP* 3.0 14.5 + - - +
68A SER* 1.3 77.4 - - - +
70A THR* 1.3 65.5 + - - +
71A TYR 3.3 2.2 - - - -
72A LEU* 3.4 28.5 + - + +
73A ARG* 3.0 23.8 + - - +
88A LEU* 5.4 0.4 - - + -
101A LEU* 3.7 29.4 - - + -
109A LEU* 5.1 2.2 - - + -
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Residues in contact with THR 70 (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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66A ASP 4.0 1.5 + - - -
67A CYS* 2.8 30.6 + - - +
68A SER 3.3 1.4 - - - -
69A LEU* 1.3 78.1 - - - +
71A TYR* 1.3 63.8 + - - +
73A ARG* 3.4 6.0 + - - +
74A LEU* 3.0 33.0 + - + +
109A LEU* 5.7 8.6 - - - +
105D ALA* 4.2 25.8 - - + -
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Residues in contact with TYR 71 (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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42A VAL* 3.9 20.2 - - + +
43A PRO 3.7 13.5 - - - -
44A PRO* 3.9 18.8 - - + -
45A GLY* 3.4 24.2 - - - -
46A ALA* 3.5 14.4 - - + -
47A PHE* 3.0 39.2 + + - +
48A ASP* 3.4 13.3 + - - -
68A SER 4.6 3.2 + - - +
69A LEU 3.3 0.8 - - - -
70A THR* 1.3 78.0 - - - +
72A LEU* 1.3 67.4 + - - +
74A LEU* 3.2 9.1 + - - +
75A TRP* 2.9 30.0 + + + +
99D ARG* 3.9 5.8 - - - +
103D TYR* 3.6 39.9 - + + +
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Residues in contact with LEU 72 (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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42A VAL* 3.9 26.4 + - + +
47A PHE* 3.9 18.4 - - + -
58A LEU* 3.8 21.8 - - + -
63A TRP* 3.9 22.0 - - + -
68A SER 5.3 0.6 + - - -
69A LEU* 3.4 34.0 + - + +
71A TYR* 1.3 83.2 - - + +
73A ARG* 1.3 57.6 + - - +
75A TRP* 3.1 6.2 + - + +
76A LEU* 2.9 43.1 + - + +
88A LEU* 3.7 23.3 - - + -
101A LEU* 5.3 0.2 - - + -
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Residues in contact with ARG 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 LEU 3.0 17.7 + - - +
70A THR* 3.7 4.9 - - - +
72A LEU* 1.3 75.5 - - - +
74A LEU* 1.3 60.0 + - + +
76A LEU* 3.2 4.9 + - - +
77A GLU* 2.9 50.5 + - + +
101A LEU* 3.4 41.0 + - + +
102A PRO* 2.9 28.9 + - - +
104A LEU 3.0 27.7 + - - -
106A GLU* 4.9 9.9 - - - +
109A LEU* 3.3 30.6 - - - +
74C LEU* 4.8 7.9 - - - +
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Residues in contact with LEU 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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70A THR* 3.0 33.0 + - + +
71A TYR* 3.5 8.1 - - - +
73A ARG* 1.3 77.1 - - + +
75A TRP* 1.3 60.1 + - - +
77A GLU* 4.0 5.2 - - + +
78A ASP* 3.3 24.8 + - - +
73D ARG* 4.9 3.8 - - - +
102D PRO 4.5 8.3 - - - +
103D TYR* 3.5 27.7 - - - +
104D LEU 3.5 27.8 - - - +
105D ALA* 4.1 5.8 - - - +
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Residues in contact with TRP 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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47A PHE* 4.0 26.4 + + + +
53A LEU* 3.7 39.2 - - + +
54A ARG 4.4 7.2 - - - -
56A ALA* 4.0 24.5 - - + -
71A TYR* 2.9 29.8 + - + +
72A LEU* 3.1 11.6 + - + +
74A LEU* 1.3 77.7 - - - +
76A LEU* 1.3 86.9 + - + +
77A GLU 3.3 0.7 + - - -
78A ASP 3.5 2.9 + - - -
82A ARG* 2.8 68.5 + - + +
100D LEU* 6.1 0.2 - - - +
103D TYR* 3.5 40.1 + + + -
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Residues in contact with LEU 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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56A ALA 4.9 2.9 - - - +
58A LEU* 4.1 15.0 - - + -
72A LEU* 2.9 46.1 + - + +
73A ARG* 3.2 7.8 + - - +
75A TRP* 1.3 103.2 - - + +
77A GLU* 1.3 58.0 + - + +
78A ASP 3.5 0.2 - - - -
82A ARG* 3.5 19.4 - - + +
85A TYR* 4.1 13.7 - - + +
86A ARG* 3.1 49.4 + - + +
88A LEU* 3.8 22.7 - - + -
101A LEU* 4.7 2.5 - - + -
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Residues in contact with GLU 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 ARG* 2.9 41.7 + - + +
74A LEU* 4.0 6.5 - - + +
75A TRP 3.2 0.4 - - - -
76A LEU* 1.3 78.0 - - + +
78A ASP* 1.3 65.2 + - - +
79A ARG 3.4 2.7 + - - -
86A ARG* 3.2 42.1 + - - +
102A PRO* 3.3 21.6 - - - +
78C ASP* 2.8 22.8 - - - +
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Residues in contact with ASP 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 LEU 3.3 17.4 + - - +
75A TRP 3.5 5.1 + - - +
76A LEU 3.5 2.4 - - - -
77A GLU* 1.3 78.2 - - - +
79A ARG* 1.3 94.9 + - - +
80A PRO* 4.8 0.3 - - - +
82A ARG* 4.1 2.5 - - - +
77D GLU* 2.8 34.5 - - - +
86D ARG* 2.9 29.9 + - - -
102D PRO* 3.7 7.7 - - - +
103D TYR* 3.8 16.2 - - + -
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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