Contacts of the strand formed by residues 38 - 51 (chain B) in PDB entry 2P80
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 VAL 38 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9B ILE* 4.5 7.4 - - + -
12B LEU* 4.7 3.9 - - + +
13B PRO 3.0 6.1 + - - -
14B ARG* 3.3 56.0 - - + +
15B GLN 3.1 21.8 + - - -
37B LYS* 1.3 68.7 - - - +
39B VAL* 1.3 62.5 + - - +
40B GLU* 4.1 3.4 - - + -
80B TYR* 3.4 25.6 - - + +
82B GLU* 4.0 33.4 - - + +
123B ARG* 4.3 9.9 - - - -
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Residues in contact with VAL 39 (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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15B GLN* 3.6 20.0 - - + +
17B VAL* 4.0 7.0 - - + -
37B LYS* 3.3 16.8 - - + +
38B VAL* 1.3 73.9 - - - +
40B GLU* 1.3 61.3 + - - +
41B PHE* 2.7 42.1 - - + -
74B VAL 4.9 2.0 - - - +
75B VAL* 3.4 29.6 - - + -
79B ASP* 4.1 7.2 - - + +
80B TYR 2.8 10.2 + - - +
81B LEU* 3.8 1.3 - - - -
82B GLU* 2.8 28.9 + - - +
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Residues in contact with GLU 40 (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* 3.6 32.2 - - + +
15B GLN 3.0 9.4 + - - +
16B LYS* 3.4 29.8 + - + +
17B VAL 3.0 24.3 + - - -
38B VAL* 3.9 12.8 - - + +
39B VAL* 1.3 79.6 - - - +
41B PHE* 1.3 65.8 + - - +
82B GLU* 3.4 21.8 - - + +
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Residues in contact with PHE 41 (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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16B LYS* 3.4 6.5 - - - +
17B VAL* 2.7 49.6 - - + -
19B LEU* 3.7 33.7 - - + -
26B HIS* 4.6 4.7 - + - -
39B VAL* 2.7 47.1 - - + -
40B GLU* 1.3 76.2 - - - +
42B THR* 1.3 59.3 + - - +
73B MET* 4.0 17.7 - - + -
74B VAL 4.4 10.3 - - - -
75B VAL* 4.0 13.5 - - + -
81B LEU* 4.2 14.1 - - + -
82B GLU 3.0 7.8 + - - +
83B LEU* 3.1 12.6 - - + +
84B THR 2.9 22.3 + - - -
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Residues in contact with THR 42 (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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16B LYS* 3.0 20.9 + - - +
17B VAL 5.2 0.4 + - - -
19B LEU* 4.4 6.1 - - - +
41B PHE* 1.3 73.1 - - - +
43B MET* 1.3 71.5 + - - +
44B VAL* 5.0 4.0 - - + -
65B ASN* 4.3 4.0 - - - +
84B THR* 3.2 31.5 + - + +
86B ILE* 4.0 22.4 - - + -
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Residues in contact with MET 43 (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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19B LEU* 3.7 19.3 - - + -
42B THR* 1.3 81.5 - - - +
44B VAL* 1.3 62.9 + - - +
64B PHE* 4.2 19.7 - - + -
65B ASN* 3.7 19.3 - - - +
71B PRO* 3.4 36.3 - - + -
73B MET* 3.8 25.6 - - + -
83B LEU* 3.8 22.4 - - + +
84B THR 3.1 7.2 + - - -
85B LEU* 3.0 26.9 - - + +
86B ILE 3.2 9.3 + - - -
97B ILE* 4.5 8.7 - - + -
134B TYR* 5.2 2.7 - - + -
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Residues in contact with VAL 44 (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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42B THR* 5.0 4.0 - - + -
43B MET* 1.3 75.6 - - - +
45B ILE* 1.3 62.4 + - - +
46B GLU* 3.8 16.2 + - + +
65B ASN* 2.9 26.2 + - - +
66B GLY 4.0 1.6 + - - -
86B ILE* 3.4 31.6 - - + +
88B PRO* 3.2 37.2 - - + -
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Residues in contact with ILE 45 (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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44B VAL* 1.3 73.6 - - - +
46B GLU* 1.3 68.4 + - - +
47B GLU* 4.8 1.1 - - + -
63B ALA 3.4 18.2 - - - +
64B PHE* 2.7 44.0 - - + -
85B LEU* 3.2 26.9 - - + -
86B ILE 3.0 15.8 + - - +
87B ASN* 4.4 4.0 - - + +
88B PRO* 3.2 10.6 - - - +
91B ASN* 2.9 22.8 + - - +
95B HIS* 4.1 24.7 - - + +
114B ILE* 4.6 3.8 - - + -
150B MET* 3.5 22.7 - - + -
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Residues in contact with GLU 46 (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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44B VAL* 3.8 15.1 + - + +
45B ILE* 1.3 80.7 - - - +
47B GLU* 1.3 65.8 + - - +
48B LYS* 3.2 25.3 + - + +
61B ALA 3.6 0.7 - - - +
63B ALA* 2.9 30.2 + - - +
66B GLY* 4.5 12.3 - - - +
88B PRO* 3.5 21.2 - - - +
90B THR* 4.3 7.7 + - - -
91B ASN* 4.1 7.3 - - - +
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Residues in contact with GLU 47 (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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45B ILE* 4.8 1.8 - - + -
46B GLU* 1.3 72.7 + - - +
48B LYS* 1.3 58.8 + - - +
60B HIS 5.7 0.7 - - - -
61B ALA 3.1 10.1 - - - +
62B MET* 4.2 14.6 - - + +
91B ASN* 3.2 28.3 + - - +
92B THR* 3.3 24.7 + - - +
93B LEU* 3.4 24.9 + - - +
95B HIS* 2.1 45.3 + - + +
199B PRO* 4.9 15.9 - - + +
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Residues in contact with LYS 48 (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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46B GLU* 3.9 23.8 - - + +
47B GLU* 1.3 76.0 - - - +
49B LYS* 1.3 69.3 + - - +
50B ILE* 4.0 22.8 + - + -
60B HIS* 3.2 6.5 - - - -
61B ALA* 2.8 31.5 + - + +
63B ALA* 5.8 2.5 - - + -
66B GLY* 3.4 31.3 + - - -
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Residues in contact with LYS 49 (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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48B LYS* 1.3 83.1 - - - +
50B ILE* 1.3 66.2 + - - +
58B GLU* 5.2 18.9 + - + +
59B VAL 3.9 6.5 - - - +
60B HIS* 3.1 40.4 - - + +
196B TYR 4.3 7.9 + - - -
197B GLU* 3.7 13.7 + - - +
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Residues in contact with ILE 50 (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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48B LYS* 4.1 27.6 - - + -
49B LYS* 1.3 80.0 - - - +
51B VAL* 1.3 66.5 + - - +
52B ILE* 4.1 8.6 - - + +
58B GLU* 3.4 2.6 - - - -
59B VAL* 3.0 38.6 + - + +
61B ALA* 3.7 21.3 - - + -
68B VAL* 4.5 16.8 - - + +
183B PHE* 5.1 5.8 - - + -
222B GLY* 4.2 20.6 - - - +
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Residues in contact with VAL 51 (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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50B ILE* 1.3 80.7 - - - +
52B ILE* 1.3 66.1 + - - +
53B ASP 3.1 25.6 - - - +
56B GLY* 3.8 20.9 - - - +
57B THR 3.2 14.4 - - - +
58B GLU* 4.4 11.9 - - + +
222B GLY 3.8 3.1 - - - +
223B ALA* 3.8 11.5 - - - +
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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