Contacts of the strand formed by residues 213 - 220 (chain B) in PDB entry 1SAW
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 213 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99B LEU* 4.4 6.3 - - + +
132B SER* 4.0 28.3 - - - +
133B ALA* 4.2 20.9 - - + +
135B VAL* 4.2 13.2 - - + -
149B TRP* 5.0 0.2 + - - -
208B GLY* 3.1 3.0 - - - -
209B ILE* 2.8 62.5 + - + +
212B LEU* 1.3 82.7 - - - +
214B SER* 1.3 77.7 + - - +
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Residues in contact with SER 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LEU* 5.9 0.4 - - - -
132B SER* 5.1 0.6 - - - -
133B ALA 5.6 1.0 + - - -
149B TRP* 4.3 19.5 + - - -
207B ALA 3.4 9.4 - - - -
208B GLY* 4.1 0.2 - - - -
209B ILE 5.0 0.5 + - - -
213B VAL* 1.3 89.1 + - - +
215B MET* 1.3 63.7 + - - +
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Residues in contact with MET 215 (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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55B GLU* 5.1 7.9 - - + -
99B LEU* 3.6 27.8 - - + +
100B CYS* 4.2 4.9 - - - -
101B LEU* 3.5 38.6 - - + +
130B PRO 4.4 2.5 - - - +
132B SER* 3.5 39.0 - - - -
206B GLU* 3.3 6.1 - - - +
207B ALA* 2.9 42.8 + - + +
214B SER* 1.3 77.9 - - - +
216B THR* 1.3 64.6 + - - +
217B PHE* 3.7 26.7 - - + -
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Residues in contact with THR 216 (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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55B GLU* 4.8 5.3 - - - +
56B GLY 4.7 8.3 + - - -
204B GLU* 3.7 36.3 - - + +
205B ILE 3.4 5.8 - - - +
206B GLU* 4.2 8.8 - - + +
215B MET* 1.3 79.3 + - - +
217B PHE* 1.3 77.1 + - - +
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Residues in contact with PHE 217 (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* 3.2 29.6 - - + -
54B PRO 3.6 11.4 - - - -
55B GLU* 3.7 12.6 - - - -
57B SER 3.3 21.1 - - - -
58B PRO 4.9 0.2 - - - -
59B ILE* 3.8 25.8 - - + -
101B LEU* 4.7 3.6 - - + -
130B PRO* 3.7 21.8 - - + -
131B VAL 3.6 18.4 - - - -
203B ASP 3.9 0.5 - - - +
204B GLU* 3.4 5.2 - - - +
205B ILE* 2.9 40.4 + - + +
215B MET* 3.7 41.7 - - + -
216B THR* 1.3 81.2 - - - +
218B LYS* 1.3 59.7 + - - +
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Residues in contact with LYS 218 (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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57B SER 5.1 0.4 + - - -
58B PRO* 3.5 11.3 - - + +
59B ILE* 2.9 25.1 + - - +
202B ASN* 6.1 1.6 - - - -
203B ASP 3.8 6.1 - - - +
204B GLU* 4.7 4.7 - - + +
217B PHE* 1.3 73.4 - - - +
219B VAL* 1.3 62.6 + - - +
220B GLU* 4.2 17.9 - - + +
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Residues in contact with VAL 219 (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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59B ILE* 3.5 22.4 - - + +
61B MET* 3.8 26.9 - - + -
199B VAL* 4.3 8.5 - - + -
200B LYS* 3.5 26.7 - - - +
201B GLU* 4.2 2.4 - - - +
202B ASN* 2.9 28.7 + - - +
203B ASP* 3.0 20.4 + - + +
205B ILE* 3.7 28.3 - - + -
217B PHE 5.1 0.2 - - - +
218B LYS* 1.3 72.6 - - - +
220B GLU* 1.3 67.6 + - - +
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Residues in contact with GLU 220 (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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58B PRO* 3.2 35.6 - - + +
59B ILE 2.9 8.5 + - - +
60B LEU* 3.5 4.9 - - + +
61B MET* 2.9 31.7 + - - +
201B GLU* 4.6 8.7 - - - -
202B ASN* 5.8 1.3 - - - +
218B LYS* 4.0 15.6 - - + +
219B VAL* 1.3 79.4 - - - +
221B LYS* 1.3 67.9 - - - +
223B GLU* 5.6 2.8 - - - +
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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