Contacts of the strand formed by residues 205 - 211 (chain B) in PDB entry 1AXS
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 THR 205 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118B GLY* 3.9 4.3 - - - -
119B PRO* 3.6 13.6 + - + +
198B VAL 3.9 1.2 - - - +
199B ASN* 3.4 2.0 - - - -
200B HIS* 2.7 56.4 + - + +
201B LYS* 4.9 0.2 - - - +
203B SER* 2.7 32.3 - - - +
204B ASN* 1.3 74.4 - - - +
206B LYS* 1.3 57.0 + - - +
207B VAL* 3.6 19.2 - - - +
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Residues in contact with LYS 206 (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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199B ASN* 3.1 26.4 + - + +
204B ASN 4.2 0.8 - - - -
205B THR* 1.3 71.4 - - - +
207B VAL* 1.3 60.9 + - - +
208B ASP* 2.8 41.2 + - + +
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Residues in contact with VAL 207 (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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119B PRO* 4.7 10.3 - - + +
121B VAL* 3.3 34.1 - - + -
196B CYS 3.4 8.5 - - - +
198B VAL* 2.6 30.7 + - + +
199B ASN* 3.6 0.4 - - - +
205B THR* 3.6 19.5 - - - +
206B LYS* 1.3 75.5 - - - +
208B ASP* 1.3 53.4 + - - +
209B LYS* 2.5 31.6 + - + +
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Residues in contact with ASP 208 (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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156B SER* 5.5 2.7 + - - +
195B ILE* 3.6 23.4 - - + +
196B CYS 4.0 4.0 - - - -
197B ASN* 4.1 13.8 - - - +
199B ASN* 3.1 11.8 + - - +
206B LYS* 2.8 42.7 + - + +
207B VAL* 1.3 67.4 - - - +
209B LYS* 1.3 56.1 + - - +
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Residues in contact with LYS 209 (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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123A GLU* 3.6 16.4 + - - -
121B VAL* 3.4 41.2 + - + +
123B PRO* 4.2 16.4 - - - +
140B CYS* 3.8 12.6 - - - -
195B ILE* 3.1 7.3 - - - +
196B CYS* 2.7 46.0 + - - +
207B VAL* 2.5 23.9 + - + +
208B ASP* 1.3 72.2 - - - +
210B LYS* 1.3 86.4 + - - +
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Residues in contact with LYS 210 (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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193B THR* 3.7 21.0 - - + +
194B TYR 2.9 17.7 - - - +
195B ILE* 3.4 15.7 - - + +
196B CYS 4.3 0.2 - - - +
209B LYS* 1.3 96.0 - - - +
211B VAL* 1.3 59.0 + - - +
212B GLU* 3.8 25.9 + - - +
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Residues in contact with VAL 211 (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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123B PRO* 3.5 24.9 - - + -
124B LEU 3.8 12.1 - - - +
125B ALA* 4.4 1.1 - - - -
138B LEU* 3.9 23.7 - - + +
139B GLY 3.1 25.8 - - - +
140B CYS* 3.3 24.9 - - - -
154B TRP* 3.7 14.6 - - + -
193B THR* 3.1 20.5 - - - +
194B TYR* 2.8 12.2 + - - +
196B CYS* 4.5 0.2 - - - -
210B LYS* 1.3 71.6 - - - +
212B GLU* 1.3 72.1 + - - +
213B PRO* 4.0 0.9 - - - +
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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