Contacts of the strand formed by residues 227 - 232 (chain A) in PDB entry 1SV6
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 ILE 227 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A VAL* 3.0 30.3 + - + +
58A GLY* 3.2 20.4 - - - -
59A ARG 3.3 8.0 + - - +
82A LEU* 4.3 6.6 - - + +
109A ALA* 4.5 13.7 - - + -
110A LEU 3.2 6.3 - - - +
111A VAL* 4.6 4.0 - - + -
164A TYR* 3.1 29.6 - - + +
166A ILE* 4.2 12.3 - - + -
225A GLY 4.6 1.1 - - - +
226A ASP* 1.3 74.5 - - - +
228A ILE* 1.3 65.9 + - - +
229A LEU* 4.1 3.4 - - + -
122D THR* 4.2 4.0 - - - +
124D ASP* 2.8 52.5 - - + +
125D GLU* 5.3 0.9 - - - +
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Residues in contact with ILE 228 (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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59A ARG 3.7 2.5 - - - -
61A VAL* 5.0 1.3 - - + -
108A ILE 3.8 0.3 - - - +
109A ALA* 3.3 4.1 - - - -
110A LEU* 2.7 47.9 + - + +
112A LEU* 3.7 28.5 - - + -
126A LEU* 5.3 4.0 - - + -
208A ALA* 4.7 21.8 - - + -
211A LEU* 3.9 21.8 - - + -
222A LEU* 3.4 35.2 - - + -
226A ASP* 5.2 0.4 - - + -
227A ILE* 1.3 77.6 - - - +
229A LEU* 1.3 66.1 + - - +
230A THR* 3.4 20.9 + - + +
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Residues in contact with LEU 229 (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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59A ARG 3.2 6.7 + - - -
60A LYS* 3.4 10.6 - - + +
61A VAL* 2.9 26.9 + - - +
82A LEU* 3.6 30.5 - - + -
107A GLU* 3.5 12.3 - - - +
108A ILE 4.1 2.2 - - - +
109A ALA* 3.7 24.2 - - + +
136A ALA* 4.0 17.9 - - + -
137A LEU 6.3 0.2 - - - -
138A GLU* 3.8 31.4 - - + -
164A TYR* 3.8 25.6 - - + -
166A ILE* 5.6 0.7 - - + -
227A ILE* 4.1 3.6 - - + -
228A ILE* 1.3 72.3 - - - +
230A THR* 1.3 61.9 + - - +
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Residues in contact with THR 230 (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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61A VAL* 3.9 4.7 - - - +
107A GLU* 2.9 19.4 - - - +
108A ILE* 2.9 34.4 + - + +
110A LEU* 4.3 16.4 - - + -
200A CYS* 4.0 13.1 - - - +
204A PRO* 3.7 28.2 - - + +
207A ALA* 4.2 8.1 - - + -
208A ALA 4.7 2.5 - - - +
228A ILE* 4.1 18.8 - - + +
229A LEU* 1.3 74.8 - - - +
231A GLY* 1.3 72.1 + - - +
233A LEU* 5.9 0.7 - - - +
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Residues in contact with GLY 231 (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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61A VAL 3.4 16.5 + - - -
62A GLY* 5.4 0.2 - - - -
64A THR* 3.1 24.0 - - - +
107A GLU* 3.2 15.5 - - - +
108A ILE 4.5 0.2 + - - -
200A CYS* 3.1 17.5 - - - +
207A ALA* 4.2 1.6 - - - +
230A THR* 1.3 88.2 + - - +
232A ALA* 1.3 63.6 + - - -
233A LEU* 3.7 2.8 + - - +
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Residues in contact with ALA 232 (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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64A THR* 3.5 9.6 + - - +
105A GLU* 3.4 37.4 + - + +
107A GLU* 3.6 10.5 + - - -
199A GLU* 4.3 13.9 - - - +
200A CYS* 4.6 0.9 + - - -
231A GLY* 1.3 73.2 - - - -
233A LEU* 1.3 64.2 + - - +
234A GLY* 3.2 16.3 + - - +
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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