Contacts of the strand formed by residues 45 - 56 (chain B) in PDB entry 1B70
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 45 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41B ILE* 3.9 10.9 - - + +
42B PRO* 3.3 14.3 + - + +
43B ARG 3.5 5.5 - - - +
44B GLY* 1.3 71.6 - - - +
46B VAL* 1.3 70.2 + - - +
88B ALA* 4.3 9.0 - - + -
89B LEU 3.4 15.5 - - - +
90B ALA* 3.9 9.9 - - + +
94B THR* 3.9 18.4 - - + -
96B LEU* 4.2 11.2 - - + -
118B LEU* 3.9 22.9 - - + -
123B LEU* 4.2 12.3 - - + -
145B PRO* 3.6 0.9 - - - +
146B LEU* 3.1 30.8 + - + +
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Residues in contact with VAL 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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43B ARG 3.9 8.1 - - - +
44B GLY 3.5 12.1 - - - +
45B VAL* 1.3 84.5 - - - +
47B PHE* 1.3 71.0 + - - +
68B ALA* 4.7 7.4 - - + +
70B ARG* 6.3 0.2 - - - +
87B VAL 3.7 0.7 - - - +
88B ALA* 3.8 2.3 - - - -
89B LEU* 2.8 49.1 + - + +
91B LEU* 3.5 19.3 - - + -
143B GLY* 3.1 29.8 - - - +
144B THR 3.6 4.3 - - - +
145B PRO* 4.1 5.4 - - + -
146B LEU* 3.9 6.1 - - - +
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Residues in contact with PHE 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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46B VAL* 1.3 76.8 - - - +
48B ALA* 1.3 70.0 + - - +
49B ARG* 4.6 1.8 - - + -
68B ALA* 4.4 0.5 - - - -
86B GLY* 3.7 23.6 - - - -
87B VAL 3.9 2.5 - - - -
88B ALA* 5.4 0.7 - - - +
135B PHE* 4.0 20.6 - + + -
136B PRO 3.6 13.5 - - - -
137B GLU 3.3 25.6 - - - -
139B ALA* 3.9 19.3 - - + -
140B LEU* 3.2 51.6 - - + -
142B PRO* 4.0 13.0 - - + -
143B GLY* 2.7 31.2 + - - -
144B THR* 3.0 16.0 + - - +
146B LEU* 4.4 9.7 - - + +
228B LEU* 5.7 0.4 - - + -
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Residues in contact with ALA 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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47B PHE* 1.3 81.5 - - - +
49B ARG* 1.3 59.3 + - - +
66B LEU* 4.3 11.7 - - + -
67B ASP 3.4 12.1 - - - +
68B ALA* 4.2 12.1 - - + -
86B GLY* 3.3 2.8 - - - -
87B VAL* 2.6 47.4 + - + +
89B LEU* 3.8 25.1 - - + -
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Residues in contact with ARG 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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47B PHE* 4.6 2.2 - - + -
48B ALA* 1.3 75.6 - - - +
50B VAL* 1.3 60.9 + - - +
51B LEU* 3.2 32.9 + - - +
66B LEU* 3.4 3.8 - - - -
67B ASP* 2.9 52.0 + - + +
85B ILE 3.5 7.4 - - - +
86B GLY* 4.5 0.7 - - - -
137B GLU* 3.3 54.5 + - + +
138B ASP* 5.9 0.8 - - - +
142B PRO* 4.2 15.5 - - + -
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Residues in contact with VAL 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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49B ARG* 1.3 68.2 - - - +
51B LEU* 1.3 60.9 + - - +
52B GLU 3.5 22.2 - - - +
53B ALA* 4.5 1.8 - - + -
64B LEU* 4.3 14.1 - - + -
66B LEU* 3.5 21.3 - - + -
81B ALA* 6.4 0.2 - - - -
82B ARG 3.5 22.9 - - - +
83B LYS* 3.8 6.5 - - - +
84B GLY* 2.9 23.6 + - - -
85B ILE* 3.0 26.2 + - + +
87B VAL* 3.7 24.9 - - + -
132B LEU* 6.0 0.4 - - + -
137B GLU* 4.7 3.8 - - - +
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Residues in contact with LEU 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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49B ARG* 3.5 36.1 - - - +
50B VAL* 1.3 73.1 - - - +
52B GLU* 1.3 74.0 + - + +
65B VAL* 2.9 22.9 + - + +
66B LEU 3.6 25.1 - - - +
67B ASP* 3.4 23.6 - - + +
71B THR* 4.2 10.3 - - + +
83B LYS* 3.4 19.3 - - - +
137B GLU* 5.8 1.6 - - - -
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Residues in contact with GLU 52 (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 VAL* 3.4 8.6 - - - +
51B LEU* 1.3 88.1 - - + +
53B ALA* 1.3 70.1 + - - +
54B HIS* 3.6 30.9 + - + -
64B LEU* 3.3 3.3 - - - -
65B VAL* 2.7 45.3 + - + -
83B LYS* 3.7 27.3 + - - +
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Residues in contact with ALA 53 (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 VAL* 4.5 0.2 - - + -
52B GLU* 1.3 85.9 + - - +
54B HIS* 1.3 62.6 + - - +
55B PRO* 3.9 6.8 - - - +
62B LYS* 4.5 14.6 + - + +
63B ARG 3.7 3.6 - - - -
64B LEU* 3.7 18.8 - - + -
82B ARG* 4.0 9.2 - - - -
83B LYS* 3.7 24.9 - - + +
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Residues in contact with HIS 54 (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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52B GLU* 3.6 39.1 + - + +
53B ALA* 1.3 72.1 - - - +
55B PRO* 1.3 70.4 - - + +
62B LYS* 3.1 2.8 - - - -
63B ARG* 2.5 87.4 + - - +
65B VAL* 4.1 5.0 - - + +
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Residues in contact with PRO 55 (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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53B ALA 3.9 5.4 - - - +
54B HIS* 1.3 90.0 - - + +
56B ILE* 1.3 63.4 + - - +
57B PRO* 3.4 8.8 - - - +
59B THR 5.6 2.5 - - - +
61B LEU 3.3 11.0 - - - +
62B LYS* 3.9 18.8 - - + +
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Residues in contact with ILE 56 (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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54B HIS 4.3 0.2 - - - +
55B PRO* 1.3 70.7 - - - +
57B PRO* 1.4 68.5 - - + +
59B THR* 2.9 47.9 + - + +
61B LEU* 2.7 34.0 + - + +
62B LYS 3.8 2.7 - - - +
63B ARG* 3.6 35.4 - - + +
75B VAL* 4.4 3.6 - - + -
109B GLN* 3.9 23.8 - - + +
111B VAL* 4.0 17.9 - - + -
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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