Contacts of the strand formed by residues 69 - 76 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B PHE* 3.1 28.4 - - - +
18B ILE* 2.8 30.5 + - + +
28B GLY 3.1 12.1 + - - -
29B GLY* 3.7 0.8 - - - -
30B GLY* 2.9 33.4 + - - +
31B ASP* 3.1 8.2 + - - +
34B ASP* 5.5 0.2 + - - -
67B LEU 3.8 0.6 + - - -
68B GLY* 1.3 72.1 - - - -
70B LEU* 1.3 75.0 + - - +
71B ILE* 4.0 12.8 - - + -
85B VAL* 4.2 8.7 - - + -
86B SER 3.4 7.2 - - - +
89B GLY 3.6 2.5 - - - -
367B ILE* 5.0 1.6 - - + -
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Residues in contact with LEU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ALA* 4.2 4.3 - - + -
16B TRP 3.7 9.2 - - - +
69B THR* 1.3 76.7 - - - +
71B ILE* 1.3 72.8 + - - +
72B VAL* 3.7 15.9 - - + -
85B VAL* 3.1 6.8 - - - -
86B SER* 2.7 38.1 + - - +
88B ALA* 3.8 12.3 - - + -
89B GLY* 3.4 18.3 - - - +
92B GLY 3.8 2.0 - - - +
93B CYS* 3.8 28.7 - - - +
96B VAL* 4.7 0.2 - - + -
135B ASN 4.8 0.2 - - - +
136B THR* 4.0 26.7 - - + -
139B CYS* 3.6 28.0 - - + -
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Residues in contact with ILE 71 (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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14B ARG 4.0 0.2 - - - +
15B ALA* 3.3 6.2 - - - +
16B TRP* 2.8 71.8 + - + +
17B PHE* 3.9 15.5 - - - -
18B ILE* 4.0 16.6 - - + +
69B THR* 3.9 14.4 - - + +
70B LEU* 1.3 76.5 - - - +
72B VAL* 1.3 70.7 + - - +
73B GLU 4.1 0.2 + - - -
83B PHE* 4.4 4.3 - - + -
84B ALA 3.5 8.5 - - - +
85B VAL* 4.1 13.5 - - + -
367B ILE* 4.4 5.4 - - + -
393B LEU* 3.9 33.9 - - + -
399B LEU* 4.3 5.8 - - + -
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Residues in contact with VAL 72 (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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13B VAL* 3.7 26.5 - - + -
14B ARG 3.6 3.1 - - - +
15B ALA* 4.8 1.6 - - + -
70B LEU* 3.7 18.2 - - + -
71B ILE* 1.3 78.8 - - - +
73B GLU* 1.3 63.5 + - - +
74B VAL* 4.2 3.4 - - + -
83B PHE* 3.0 7.0 - - - +
84B ALA 3.0 31.5 + - - -
96B VAL* 4.0 17.5 - - + -
139B CYS* 3.6 30.7 - - + +
140B VAL* 4.2 14.6 - - + -
143B ALA* 3.7 13.9 - - + +
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Residues in contact with GLU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B HIS 4.1 0.3 - - - +
13B VAL* 3.5 2.8 - - - +
14B ARG* 2.9 50.3 + - + +
16B TRP* 3.6 29.5 - - + -
71B ILE* 4.1 1.3 + - + -
72B VAL* 1.3 76.7 - - - +
74B VAL* 1.3 64.4 + - - +
75B GLU* 5.0 1.3 - - + +
81B THR* 3.9 30.3 + - + +
82B GLY 3.4 11.0 - - - +
83B PHE* 4.0 9.6 - - + +
393B LEU* 4.5 3.8 - - + +
395B ARG* 2.8 39.5 + - - -
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Residues in contact with VAL 74 (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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10B ILE* 3.6 24.5 - - + -
12B HIS 3.6 4.3 - - - +
13B VAL* 3.8 18.6 - - + -
72B VAL* 4.2 2.5 - - + -
73B GLU* 1.3 78.6 - - - +
75B GLU* 1.3 61.6 + - - +
81B THR* 3.1 5.4 - - - -
82B GLY 2.8 39.4 + - - +
104B ILE* 4.4 4.7 - - + -
140B VAL* 5.0 2.7 - - + +
143B ALA* 3.9 23.3 - - + +
144B LEU* 4.1 22.7 - - + -
147B LEU* 3.5 24.1 - - + +
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Residues in contact with GLU 75 (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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10B ILE* 3.8 0.7 - - - -
11B LYS* 2.7 33.6 + - + +
12B HIS* 2.8 33.5 + - + +
14B ARG* 2.2 44.7 + - - +
73B GLU* 4.2 1.5 + - - +
74B VAL* 1.3 73.6 - - - +
76B ALA* 1.3 65.3 + - - +
79B ARG* 3.5 33.5 + - - +
80B GLN 3.5 8.5 - - - +
81B THR* 3.7 16.2 - - + -
147B LEU* 4.5 2.7 - - - -
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Residues in contact with ALA 76 (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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8B PRO* 3.6 16.8 - - + -
9B LYS 3.4 13.0 - - - +
10B ILE* 4.2 1.8 - - - +
11B LYS* 4.1 3.3 - - - +
75B GLU* 1.3 87.0 - - - +
77B GLU* 1.3 60.6 + - - +
78B ASN* 3.1 19.1 - - - +
79B ARG* 3.0 15.6 + - - +
80B GLN 2.7 14.0 + - - +
109B VAL* 4.1 12.3 - - + -
147B LEU* 4.1 10.8 - - + +
151B VAL* 4.6 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
------------------------------------------------------------
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