Contacts of the strand formed by residues 708 - 712 (chain A) in PDB entry 1SIW
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 ASN 708 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A TRP* 5.0 0.2 - - - -
172A SER* 2.8 37.8 + - - +
173A ASN* 3.0 29.7 + - - +
176A THR* 3.3 15.2 + - - -
184A ARG 3.2 3.7 + - - +
185A VAL* 3.5 13.8 - - + -
186A ALA* 2.7 34.3 + - - +
706A PRO* 5.2 1.3 - - - +
707A ARG* 1.3 103.9 + - - +
709A LEU* 1.3 57.4 + - - +
710A PHE* 5.4 2.7 - - + -
765A LEU* 4.9 1.1 - - - -
766A ASP* 4.0 4.8 - - - +
767A LEU* 3.5 17.6 - - + +
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Residues in contact with LEU 709 (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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186A ALA* 3.3 22.0 - - + +
187A GLY* 4.2 0.9 - - - +
188A PHE* 4.2 8.7 - - + +
214A LEU* 4.4 10.1 - - + -
610A TYR* 5.5 2.7 - - + +
611A PHE* 5.3 7.4 - - + -
706A PRO* 6.3 0.4 - - + -
707A ARG 4.2 0.2 - - - -
708A ASN* 1.3 74.7 - - - +
710A PHE* 1.3 77.9 + - - +
711A ILE* 3.8 27.4 - - + -
716A LEU* 4.3 12.1 - - + -
717A LEU* 5.4 4.9 - - + -
731A LEU* 5.6 1.6 - - + -
765A LEU* 3.9 35.2 - - + +
767A LEU 3.0 10.2 + - - +
768A VAL* 3.5 6.4 - - + +
769A VAL* 3.0 28.3 + - - +
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Residues in contact with PHE 710 (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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169A ILE* 3.5 26.7 - - + -
173A ASN* 3.4 34.5 - - - -
185A VAL* 4.2 10.3 - - + -
186A ALA 2.8 18.3 + - - +
187A GLY* 4.0 6.1 - - - -
188A PHE 2.7 32.2 + - - -
205A TYR* 4.0 17.5 - + - -
206A LEU* 4.0 13.5 - - + -
708A ASN* 5.2 2.2 - - + -
709A LEU* 1.3 76.6 - - - +
711A ILE* 1.3 60.6 + - - +
712A TRP* 4.1 4.0 - - + -
767A LEU* 6.2 0.2 - - + -
769A VAL* 3.5 28.5 - - + -
771A LEU* 5.0 1.1 - - + -
826A TYR* 3.6 35.7 - + + +
829A ILE* 4.9 4.3 - - + -
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Residues in contact with ILE 711 (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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188A PHE* 3.5 7.2 - - + +
709A LEU* 3.8 28.9 - - + -
710A PHE* 1.3 80.3 - - - +
712A TRP* 1.3 61.5 + - - +
714A SER* 3.8 36.1 - - - +
716A LEU* 4.1 18.8 - - + -
717A LEU* 4.2 7.0 - - + -
768A VAL* 4.1 15.7 - - + -
769A VAL 2.9 8.9 + - - +
770A THR* 3.4 11.8 - - + +
771A LEU* 3.0 26.0 + - - +
778A THR* 3.8 26.7 - - + -
826A TYR* 4.8 0.8 + - - -
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Residues in contact with TRP 712 (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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187A GLY* 3.8 11.9 - - - -
188A PHE 3.3 29.7 + - - +
189A SER* 2.5 51.0 + - - -
198A SER 3.0 27.3 + - - -
199A TYR* 3.4 16.4 + + - +
201A SER* 3.9 3.4 + - - -
202A GLY* 3.4 23.8 - - - -
203A ALA* 3.5 14.1 - - + -
206A LEU* 4.0 10.8 - - + -
213A CYS* 6.2 0.4 - - - -
710A PHE* 3.8 5.2 - - + -
711A ILE* 1.3 78.4 - - - +
713A ARG* 1.3 83.1 + - + +
714A SER 3.0 3.1 + - - +
771A LEU* 3.8 27.4 - - + -
822A ASP* 4.2 7.4 - - - -
826A TYR* 3.2 26.7 - + - +
1247A GDP 3.8 2.2 - - - +
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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