Contacts of the strand formed by residues 209 - 216 (chain C) in PDB entry 4AOR
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 LYS 209 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C ILE* 4.4 0.2 - - - -
127C SER* 3.3 17.6 + - - +
128C LEU 3.9 15.6 + - - +
129C PRO* 4.0 18.4 - - + -
130C THR* 5.0 14.0 + - - +
205C VAL* 3.3 6.5 - - - +
206C CYS 2.9 32.5 + - - +
207C SER* 3.5 18.2 - - - +
208C GLY* 1.3 85.9 - - - +
210C LEU* 1.3 60.4 + - - +
211C GLN* 3.1 18.9 + - - +
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Residues in contact with LEU 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C SER* 3.5 36.6 - - - +
53C ILE* 4.2 11.9 - - + -
59C VAL* 4.2 21.8 - - + -
126C ILE* 3.9 10.8 - - + +
127C SER 2.9 18.2 + - - +
128C LEU* 4.5 8.5 - - + -
129C PRO* 3.0 23.1 - - - +
203C PRO* 3.8 11.7 - - + -
204C VAL 3.7 7.4 - - - +
205C VAL* 4.2 6.1 - - + -
209C LYS* 1.3 68.2 - - - +
211C GLN* 1.3 60.0 + - - +
212C GLY 3.5 23.8 - - - +
213C ILE* 5.2 1.6 - - + -
232C VAL* 3.4 19.6 - - + +
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Residues in contact with GLN 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C PRO* 3.4 25.3 - - - +
131C SER 3.1 21.1 + - - +
132C CYS* 4.1 0.2 - - - -
133C ALA* 3.8 30.3 + - + +
165C ILE* 5.1 0.9 - - + -
184C PHE* 3.5 16.6 - - + -
204C VAL 2.9 5.1 + - - -
206C CYS* 3.9 30.8 + - + -
209C LYS* 3.1 23.4 + - + +
210C LEU* 1.3 75.3 - - - +
212C GLY* 1.3 59.5 + - - +
230C THR 3.4 1.0 - - - +
231C LYS* 3.6 1.2 - - - +
232C VAL* 2.8 27.1 + - - +
233C CYS* 3.8 14.2 + - - +
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Residues in contact with GLY 212 (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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184C PHE* 3.7 10.3 - - - -
202C GLY 3.9 0.2 - - - +
203C PRO 3.8 0.3 - - - -
204C VAL* 2.9 40.4 + - - +
210C LEU* 3.5 13.4 - - - +
211C GLN* 1.3 80.3 - - - +
213C ILE* 1.3 65.4 + - - +
229C TYR* 4.3 0.4 - - - -
230C THR 3.1 9.0 - - - -
232C VAL* 4.0 1.1 - - - -
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Residues in contact with ILE 213 (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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59C VAL* 3.6 29.4 - - + -
60C SER 3.8 13.5 - - - +
61C ALA* 3.8 5.8 - - + +
107C ASP 4.1 0.4 - - - +
108C ILE* 3.6 22.9 - - + -
201C GLY* 3.5 31.4 - - - +
202C GLY 3.3 5.4 - - - +
210C LEU* 5.2 2.0 - - + -
212C GLY* 1.3 77.7 - - - +
214C VAL* 1.3 69.8 + - - +
215C SER* 3.1 1.9 + - - -
229C TYR* 3.3 7.7 - - - +
230C THR* 3.0 43.8 + - + +
232C VAL* 3.7 19.3 - - + -
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Residues in contact with VAL 214 (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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61C ALA* 4.1 4.0 - - - +
63C HIS* 4.2 0.2 - - - -
141C ILE* 4.2 16.6 - - + -
142C SER 4.9 1.8 - - - +
195C SER* 3.6 20.2 - - - +
199C ASP* 3.3 42.4 - - + +
200C SER* 3.7 5.9 - - - +
201C GLY* 2.9 23.5 + - - +
202C GLY* 2.9 27.1 + - - +
203C PRO 4.5 0.9 - - - +
204C VAL* 4.7 0.2 - - - +
213C ILE* 1.3 73.9 - - - +
215C SER* 1.3 61.5 + - - +
229C TYR* 3.5 18.5 - - + -
32F ARG* 3.9 14.6 - - + -
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Residues in contact with SER 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C HIS* 3.2 16.0 + - - -
104C LEU* 4.8 1.2 + - - +
107C ASP* 2.6 29.0 + - - +
200C SER* 3.7 0.2 + - - -
213C ILE 3.1 7.9 + - - -
214C VAL* 1.3 77.2 - - - +
216C TRP* 1.3 80.8 + - - +
228C VAL 3.4 14.2 + - - -
229C TYR* 4.5 0.6 - - - -
230C THR* 3.8 14.4 - - - -
31F LEU* 3.7 1.2 - - - -
32F ARG* 3.2 24.3 + - - +
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Residues in contact with TRP 216 (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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104C LEU* 3.6 27.9 - - + +
175C TYR* 3.7 41.5 - + + -
178C GLN* 4.0 31.4 - - + -
179C ILE* 4.0 3.6 - - + -
183C MET* 3.8 16.9 - - + +
215C SER* 1.3 104.6 - - - +
217C GLY* 1.3 81.1 + - - +
228C VAL* 2.8 57.6 + - + +
1247C GOL 3.4 30.1 - - - -
30F ILE* 3.3 28.9 - - + +
31F LEU* 4.2 0.9 - - - -
32F ARG* 3.7 15.6 + - - +
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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