Contacts of the strand formed by residues 69 - 76 (chain A) in PDB entry 2P3Z
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 THR 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A PHE* 3.0 10.0 - - - +
18A ILE* 2.9 50.5 + - + +
27A ALA* 5.7 0.2 - - - +
28A GLY 3.1 14.7 + - - -
30A GLY* 2.9 33.7 + - - +
31A ASP 3.2 4.2 + - - +
67A LEU 3.9 0.2 + - - -
68A GLY* 1.3 71.5 - - - -
70A LEU* 1.3 73.9 + - - +
71A ILE* 4.1 12.3 - - + -
85A VAL* 4.2 6.7 - - + -
86A SER 3.4 8.7 - - - +
89A GLY 3.7 3.4 - - - -
367A ILE* 4.8 2.0 - - + -
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Residues in contact with LEU 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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15A ALA* 3.9 8.3 - - + -
16A TRP 3.7 11.0 - - - +
69A THR* 1.3 75.8 - - - +
71A ILE* 1.3 74.1 + - - +
72A VAL* 3.8 13.0 - - + -
85A VAL* 3.2 5.5 - - - -
86A SER* 2.9 36.2 + - - +
88A ALA* 3.9 11.4 - - + -
89A GLY* 3.4 17.6 - - - +
92A GLY* 3.8 1.8 - - - -
93A CYS* 3.6 29.2 - - - +
135A ASN 4.8 0.4 - - - +
136A THR* 3.9 28.7 - - + +
139A CYS* 3.7 26.0 - - + -
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Residues in contact with ILE 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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14A ARG 3.9 0.3 - - - +
15A ALA* 3.1 7.6 - - - +
16A TRP* 2.8 53.0 + - + +
17A PHE* 4.4 1.3 - - - -
18A ILE* 3.9 20.0 - - + -
69A THR* 4.1 11.0 - - + +
70A LEU* 1.3 79.0 - - - +
72A VAL* 1.3 66.8 + - - +
73A GLU 4.2 0.2 - - - -
83A PHE* 4.4 7.0 - - + -
84A ALA 3.5 7.9 - - - +
85A VAL* 3.8 14.6 - - + -
367A ILE* 3.9 25.6 - - + -
393A LEU* 3.8 31.2 - - + -
399A LEU* 4.1 11.0 - - + -
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Residues in contact with VAL 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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13A VAL* 3.8 23.8 - - + -
14A ARG 3.4 3.6 - - - +
15A ALA* 4.7 2.5 - - + -
70A LEU* 3.8 17.7 - - + -
71A ILE* 1.3 77.2 - - - +
73A GLU* 1.3 61.6 + - - +
74A VAL* 4.4 2.0 - - + -
83A PHE* 3.0 24.8 - - - +
84A ALA 3.1 10.1 + - - -
96A VAL* 3.9 19.7 - - + -
139A CYS* 3.7 30.3 - - + +
140A VAL* 4.0 16.4 - - + -
143A ALA* 3.6 15.6 - - + +
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Residues in contact with GLU 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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12A HIS 4.1 0.3 - - - +
13A VAL* 3.4 2.8 - - - +
14A ARG* 2.9 58.6 + - + +
16A TRP* 3.7 24.5 - - + -
71A ILE* 4.2 2.2 - - + -
72A VAL* 1.3 74.0 - - - +
74A VAL* 1.3 64.0 + - - +
75A GLU* 4.3 0.4 + - + -
81A THR* 3.8 29.6 + - + +
82A GLY 3.3 12.1 - - - +
83A PHE* 4.0 9.8 - - + +
393A LEU* 4.4 5.5 - - + +
395A ARG* 2.9 39.0 + - - -
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Residues in contact with VAL 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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10A ILE* 3.2 40.8 - - + -
12A HIS 3.4 3.1 - - - +
13A VAL* 3.7 22.4 - - + -
72A VAL* 4.4 3.1 - - + -
73A GLU* 1.3 72.6 - - - +
75A GLU* 1.3 59.3 + - - +
81A THR* 3.3 5.4 - - - -
82A GLY 2.8 33.3 + - - +
104A ILE* 4.5 4.3 - - + -
140A VAL* 5.1 2.0 - - + +
143A ALA* 4.1 21.8 - - + +
144A LEU* 4.2 18.2 - - + +
147A LEU* 3.4 22.8 - - + +
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Residues in contact with GLU 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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10A ILE* 3.5 3.3 - - - +
11A LYS* 2.6 34.5 + - - +
12A HIS* 2.7 35.2 + - + +
14A ARG* 2.3 44.0 + - - +
73A GLU* 4.2 0.9 - - + +
74A VAL* 1.3 73.4 - - - +
76A ALA* 1.3 63.7 + - - +
79A ARG* 3.6 32.2 + - - +
80A GLN 3.5 4.7 - - - +
81A THR* 3.7 21.5 - - + -
147A LEU* 4.6 0.4 - - - -
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Residues in contact with ALA 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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8A PRO* 3.9 14.8 - - + -
9A LYS 3.4 13.5 - - - +
10A ILE* 4.1 2.2 - - - +
11A LYS* 3.9 4.5 - - - +
74A VAL 4.2 0.6 - - - -
75A GLU* 1.3 82.9 - - - +
77A GLU* 1.3 60.8 + - - +
78A ASN* 3.2 20.9 - - - +
79A ARG* 2.9 20.8 + - - +
80A GLN* 2.9 13.8 + - + +
109A VAL* 4.1 12.3 - - + -
147A LEU* 4.3 9.7 - - + +
151A VAL* 4.8 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