Contacts of the strand formed by residues 82 - 90 (chain A) in PDB entry 3S1R
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 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A VAL* 5.0 1.4 - - - +
31A SER* 3.7 9.3 - - - -
32A VAL 4.2 3.1 - - - -
33A ALA 4.5 1.6 - - - -
35A ILE* 3.8 13.7 - - - -
58A LEU* 3.8 10.4 - - - +
80A HIS 3.7 1.6 + - - -
81A PHE* 1.3 77.8 - - - +
83A HIS* 1.3 59.5 + - - +
240A PRO* 3.7 4.7 - - - +
241A VAL* 2.8 37.1 + - - -
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Residues in contact with HIS 83 (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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27A VAL* 3.9 20.6 - - + +
28A ARG* 3.8 16.8 - - + +
31A SER* 3.1 22.1 + - - -
33A ALA 3.0 29.6 + - - -
34A LYS* 3.0 30.1 + - - +
35A ILE* 3.4 14.7 - - - +
82A GLY* 1.3 74.0 - - - +
84A ILE* 1.3 60.9 + - - +
85A ASP* 3.4 30.4 + - - -
238A CYS* 3.2 20.2 - - - -
239A LEU 3.6 5.4 - - - -
241A VAL* 3.6 4.7 - - - -
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Residues in contact with ILE 84 (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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34A LYS 4.4 3.6 - - - -
35A ILE* 4.2 12.3 - - + +
83A HIS* 1.3 78.8 - - - +
85A ASP* 1.3 65.9 + - - +
86A LEU* 3.5 6.1 + - + +
238A CYS* 3.8 3.3 - - - -
239A LEU* 3.2 58.7 + - + +
241A VAL* 3.7 16.2 - - + -
266A LEU* 5.2 1.8 - - + +
269A ILE* 4.1 21.1 - - + -
270A LEU* 3.6 40.6 - - + -
273A ASN* 4.3 19.1 - - + +
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Residues in contact with ASP 85 (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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28A ARG* 2.7 40.1 + - - +
34A LYS* 5.0 5.1 + - - +
83A HIS* 3.4 24.3 + - - -
84A ILE* 1.3 70.7 - - - +
86A LEU* 1.3 59.4 + - - +
237A THR 4.6 2.5 - - - -
238A CYS* 3.7 0.9 - - - -
273A ASN* 2.9 27.5 + - - -
277A GLU* 3.6 9.4 - - - +
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Residues in contact with LEU 86 (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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84A ILE* 3.5 6.5 + - + +
85A ASP* 1.3 73.9 - - - +
87A ALA* 1.4 65.3 + - - +
88A LYS 4.5 10.1 - - - +
89A PRO* 5.1 1.8 - - + +
90A VAL* 4.2 4.9 - - + -
236A LEU* 3.5 28.3 - - + +
237A THR* 3.4 33.9 + - - +
239A LEU* 3.9 25.4 - - + +
269A ILE* 5.0 6.1 - - + -
273A ASN* 3.5 6.3 - - + +
296A LEU* 3.9 27.8 - - + -
300A VAL* 3.9 23.6 - - + -
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Residues in contact with ALA 87 (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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85A ASP 3.8 0.8 + - - -
86A LEU* 1.4 73.8 - - - +
88A LYS* 1.4 59.3 + - - +
89A PRO* 4.0 4.9 - - - +
205A GLU* 5.3 0.3 - - - +
273A ASN* 3.1 11.7 + - - +
276A LEU* 3.7 33.4 - - + -
277A GLU* 3.8 23.5 + - + -
280A GLU* 4.2 10.7 - - - +
296A LEU* 4.7 1.0 - - - +
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Residues in contact with LYS 88 (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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86A LEU* 4.5 3.5 - - - +
87A ALA* 1.4 78.2 - - - +
89A PRO* 1.4 68.8 - - - +
90A VAL* 3.3 5.0 + - - +
203A SER* 4.4 13.6 + - - -
204A THR* 5.6 1.3 - - - -
205A GLU* 3.3 40.2 - - + +
276A LEU* 4.0 20.9 - - + +
280A GLU* 5.8 4.5 - - - +
290A GLU* 2.7 29.5 + - - -
293A GLU* 3.5 35.3 + - + +
296A LEU* 3.5 19.8 - - + +
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Residues in contact with PRO 89 (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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86A LEU* 5.1 4.2 - - + +
87A ALA 4.0 6.1 - - - +
88A LYS* 1.4 81.5 - - - +
90A VAL* 1.4 58.9 + - - +
204A THR* 3.2 24.9 - - - +
205A GLU* 3.4 36.9 - - + +
208A LEU* 3.8 33.0 - - + -
235A ILE* 5.1 2.2 - - + -
236A LEU 3.7 9.0 - - - +
237A THR* 3.9 22.4 - - + -
293A GLU* 4.4 1.6 - - - +
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Residues in contact with VAL 90 (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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86A LEU* 4.2 12.1 - - + -
88A LYS 3.6 10.1 - - - +
89A PRO* 1.4 71.4 - - - +
91A PHE* 1.4 59.6 + - - +
204A THR* 3.8 1.6 - - - -
235A ILE* 3.4 8.5 - - - +
236A LEU* 2.7 42.7 + - + +
293A GLU* 3.4 23.3 - - - +
296A LEU* 3.8 8.5 - - + -
297A GLN* 3.4 33.2 - - - +
300A VAL* 3.8 39.5 - - + -
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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