Contacts of the strand formed by residues 201 - 209 (chain C) in PDB entry 6UWZ
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 ASP 201 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197C TRP* 5.7 0.2 - - - +
198C ARG* 2.6 37.5 + - + +
200C ASP* 1.3 88.5 + - - +
202C PRO* 1.3 66.0 - - - +
203C SER* 2.9 28.8 + - - -
204C TYR* 3.3 22.8 + - + +
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Residues in contact with PRO 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C THR* 3.5 16.7 + - - +
197C TRP* 5.6 1.7 - - - -
198C ARG 4.4 1.3 - - - +
199C SER 4.6 7.0 - - - +
200C ASP 3.6 10.5 - - - +
201C ASP* 1.3 88.2 - - - +
203C SER* 1.3 58.2 + - - +
204C TYR 3.3 3.5 + - - +
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Residues in contact with SER 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C LYS* 5.5 2.6 + - - -
152C ASP* 3.5 37.6 - - - +
153C THR* 3.5 20.0 + - - +
201C ASP* 2.9 22.4 + - - -
202C PRO* 1.3 78.4 - - - +
204C TYR* 1.3 60.7 + - - +
205C GLU 3.9 0.9 + - - -
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Residues in contact with TYR 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C MET* 6.1 0.2 - - - +
145C VAL* 3.9 10.2 - - - +
147C LYS* 3.5 30.4 - - + +
153C THR* 4.1 2.6 - - - +
196C ASN* 3.7 14.6 - - + -
197C TRP* 3.4 21.8 - - - -
198C ARG* 3.7 56.5 + - + -
201C ASP* 3.7 30.5 - - + +
202C PRO 3.3 3.7 - - - +
203C SER* 1.3 80.0 + - - +
205C GLU* 1.3 63.0 + - - +
206C ASP* 2.5 42.2 + - + +
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Residues in contact with GLU 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C LYS* 3.5 21.4 - - - +
153C THR* 4.1 18.6 - - + +
156C VAL 4.4 1.7 - - - +
157C THR* 4.3 12.5 - - - +
158C LEU* 3.4 41.6 + - + +
195C LYS* 3.3 28.9 + - + -
196C ASN 3.6 5.6 - - - +
197C TRP* 3.5 27.3 + - + +
203C SER 3.9 2.4 + - - -
204C TYR* 1.3 79.5 - - - +
206C ASP* 1.3 67.5 + - - +
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Residues in contact with ASP 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C VAL* 3.9 13.1 - - + +
146C PHE 3.4 12.3 - - - +
147C LYS* 4.1 4.3 - - + -
158C LEU* 4.4 1.3 - - - -
195C LYS* 3.1 9.2 - - - +
196C ASN* 3.0 44.2 + - - +
204C TYR* 2.5 36.7 + - + +
205C GLU* 1.3 74.9 - - - +
207C VAL* 1.3 62.5 + - - +
208C THR* 2.6 27.2 + - - -
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Residues in contact with VAL 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C VAL* 3.9 19.7 - - + +
146C PHE* 2.9 35.9 + - - +
158C LEU* 3.8 20.8 - - + +
159C GLN 3.7 20.0 - - - +
160C HIS* 4.5 8.7 - - + +
193C SER* 3.7 20.6 - - - +
194C ARG 3.8 3.1 - - - +
195C LYS* 3.8 16.2 - - + -
206C ASP* 1.3 75.0 - - - +
208C THR* 1.3 59.5 + - - +
209C PHE* 3.7 20.9 - - + -
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Residues in contact with THR 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C THR* 3.9 10.8 - - - +
144C MET 3.6 5.2 - - - +
145C VAL* 3.7 26.3 - - + +
193C SER* 3.2 24.6 + - - -
194C ARG 3.0 11.2 + - - -
196C ASN* 2.8 19.3 + - - +
206C ASP* 2.6 31.2 + - - -
207C VAL* 1.3 73.2 - - - +
209C PHE* 1.3 63.9 + - - +
210C TYR* 3.5 26.8 - - + +
2J NAG 5.2 2.0 - - + +
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Residues in contact with PHE 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C VAL* 3.6 28.9 - - + -
34C GLY* 3.8 7.0 - - - -
35C LEU* 3.6 33.4 - - + -
143C THR* 3.1 2.3 - - - -
144C MET* 2.5 45.7 + - + +
146C PHE* 3.6 30.1 - + - -
170C VAL 6.0 1.1 - - - -
172C GLU 4.8 6.7 - - - -
173C ILE* 3.6 33.0 - - + -
192C PRO 3.7 2.0 - - - -
193C SER* 3.3 27.4 - - - -
207C VAL* 3.7 19.7 - - + -
208C THR* 1.3 73.2 - - - +
210C TYR* 1.3 60.3 + - - +
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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