Contacts of the strand formed by residues 41 - 48 (chain B) in PDB entry 1SPD
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 GLY 41 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B THR 5.0 0.4 - - - -
40B GLU* 1.4 85.7 - - - +
42B LEU* 1.4 59.5 + - - -
43B HIS 4.3 0.2 - - - -
88B THR* 2.7 44.5 - - - +
89B ALA 3.0 18.6 + - - +
90B ASP* 5.4 0.2 - - - +
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Residues in contact with LEU 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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40B GLU 2.9 10.1 + - - -
41B GLY* 1.4 80.3 - - - +
43B HIS* 1.4 71.4 + - - +
86B ASN* 2.5 41.3 - - + +
87B VAL 3.6 7.9 - - - +
88B THR* 3.7 15.5 - - + -
122B LYS 3.1 14.6 - - - +
123B ALA* 3.2 24.2 + - + +
124B ASP 5.9 0.4 - - - +
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Residues in contact with HIS 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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38B LEU* 3.9 31.2 - - + +
39B THR* 2.2 50.0 + - - -
40B GLU 4.8 1.0 + - - -
41B GLY 5.1 0.2 - - - -
42B LEU* 1.4 81.5 + - - +
44B GLY* 1.4 56.5 + - - +
86B ASN* 2.8 40.3 - - - -
87B VAL* 2.8 32.2 + - + +
89B ALA* 4.5 3.8 - - + -
119B VAL* 5.1 2.7 - - + -
120B HIS 3.1 17.5 + - - +
121B GLU* 2.8 27.5 + - - -
122B LYS* 3.6 2.9 + - - -
144B LEU* 5.6 4.3 - - + -
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Residues in contact with GLY 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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43B HIS* 1.4 70.7 - - - +
45B PHE* 1.4 67.2 - - - +
46B HIS 3.8 1.8 - - - -
85B GLY 3.3 8.1 - - - -
119B VAL* 3.2 9.9 - - - +
120B HIS* 2.7 52.9 + - - -
122B LYS 3.4 5.3 + - - -
124B ASP* 3.9 12.3 - - - -
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Residues in contact with PHE 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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18B ILE* 2.8 37.9 - - + -
31B VAL* 4.7 12.8 - - + -
35B ILE* 3.3 28.3 - - + -
43B HIS 4.4 0.4 - - - +
44B GLY* 1.4 71.3 - - - -
46B HIS* 1.4 64.0 - - - +
84B LEU* 2.7 56.8 + - + +
85B GLY 3.0 20.4 + - - +
87B VAL* 3.2 34.1 - - + -
97B VAL* 5.3 1.6 - - + -
99B ILE* 5.4 4.3 - - + -
117B LEU* 4.2 26.9 - - + -
118B VAL 4.3 0.4 - - - -
119B VAL* 3.4 25.1 - - + -
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Residues in contact with HIS 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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45B PHE* 1.4 90.5 - - - +
47B VAL* 1.3 62.2 - - - +
48B HIS* 3.7 2.0 - - - +
63B HIS* 2.1 43.4 + + + -
71B HIS* 3.1 20.6 - + - -
82B GLY 3.3 4.5 - - - -
83B ASP* 3.2 25.0 - - + +
84B LEU 4.0 0.2 - - - -
85B GLY 4.4 1.8 - - - -
117B LEU* 3.0 13.9 - - - +
118B VAL 2.8 34.9 + - - +
120B HIS* 3.1 16.5 + + - +
124B ASP* 2.6 24.3 + - - -
137B THR 4.5 6.1 - - - -
140B ALA* 4.8 0.7 - - + -
154B CU 2.2 15.8 - - - -
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Residues in contact with VAL 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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20B PHE* 4.7 1.8 - - + -
46B HIS* 1.3 77.7 - - - +
48B HIS* 1.3 52.8 + - - +
63B HIS* 3.6 1.3 - - - -
64B PHE* 2.7 37.6 + - + -
82B GLY* 2.7 24.7 + - - +
84B LEU* 4.3 15.7 - - + -
104B ILE* 5.1 3.6 - - + -
112B ILE* 4.1 29.6 - - + -
115B ARG* 4.5 10.5 - - + -
116B THR 3.1 18.2 - - - +
117B LEU* 3.5 24.9 - - + -
149B ILE* 4.1 4.9 - - + -
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Residues in contact with HIS 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 HIS* 3.7 5.2 - - + -
47B VAL* 1.3 70.4 - - - +
49B GLU* 1.3 61.2 - - - +
50B PHE 3.6 0.2 + - - -
60B ALA* 2.9 26.1 - - + +
61B GLY 2.5 19.8 + - - +
62B PRO* 3.2 13.9 + - + +
63B HIS* 2.8 24.1 + + - -
115B ARG* 4.5 1.1 - - - -
116B THR* 2.7 40.8 + - - +
118B VAL* 3.0 26.9 - - + +
120B HIS* 3.1 4.9 + + - -
137B THR* 4.8 4.5 - - + -
143B ARG* 3.1 21.8 - - - +
154B CU 2.1 31.8 - - - -
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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