Contacts of the strand formed by residues 16 - 21 (chain 9) in PDB entry 1O19
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 LEU 16 (chain 9).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139 GLY* 3.1 17.6 + - - -
159 GLY* 1.3 82.2 - - - +
179 VAL* 1.3 59.3 + - - +
189 LYS* 2.7 39.4 + - + +
309 VAL* 3.8 16.4 - - + -
319 PHE* 3.5 29.2 - - - +
329 PRO* 3.8 8.7 - - + -
339 SER* 4.6 1.8 - - - -
1579 ASP* 5.2 5.3 - - + +
2109 ARG* 6.1 2.2 - - - +
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Residues in contact with VAL 17 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109 CYS* 4.1 24.0 - - - -
119 ASP 3.5 11.4 - - - +
129 ASN* 4.5 8.5 - - - +
139 GLY 4.6 0.4 - - - +
169 LEU* 1.3 74.5 - - - +
189 LYS* 1.3 70.0 + - - +
299 ALA 4.2 0.7 - - - -
309 VAL* 3.2 24.4 - - - +
319 PHE* 3.0 38.2 + - + +
339 SER* 4.0 13.5 - - - +
829 MET* 5.8 0.4 - - + -
859 ILE* 3.7 28.7 - - + -
899 THR* 4.5 8.1 - - + +
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Residues in contact with LYS 18 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109 CYS* 3.6 0.3 - - - -
119 ASP* 2.8 60.6 + - + +
139 GLY* 4.3 7.7 - - - -
169 LEU* 2.7 40.7 + - + +
179 VAL* 1.3 76.9 - - - +
199 ALA* 1.3 61.6 + - - +
279 PRO* 4.0 6.7 - - + -
299 ALA 3.3 4.9 - - - -
309 VAL* 4.2 7.0 - - + -
3369 LYS 5.1 4.7 - - - +
3379 TYR* 3.8 33.7 - - + -
3409 TRP* 3.4 22.1 - - + -
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Residues in contact with ALA 19 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99 VAL 3.2 11.0 - - - +
109 CYS* 4.6 5.4 - - + -
179 VAL* 4.7 3.6 - - + -
189 LYS* 1.3 74.1 - - - +
209 GLY* 1.3 52.7 + - - +
279 PRO* 3.2 4.7 - - - +
289 ARG 2.6 30.5 + - - -
299 ALA* 2.7 27.1 + - + +
899 THR* 3.6 31.4 - - + -
949 LEU* 4.0 6.5 - - + -
3409 TRP* 3.6 4.5 - - - +
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Residues in contact with GLY 20 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89 LEU* 3.6 7.3 - - - +
99 VAL 3.0 24.8 + - - -
199 ALA* 1.3 78.4 - - - +
219 PHE* 1.3 66.3 + - - -
249 ASP* 4.4 0.2 - - - -
289 ARG* 3.7 18.6 - - - -
949 LEU* 3.6 12.7 - - - +
3409 TRP* 3.6 10.5 - - - -
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Residues in contact with PHE 21 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59 THR 3.8 22.7 - - - +
79 ALA 3.5 2.5 - - - -
89 LEU* 3.5 28.9 - - + -
209 GLY* 1.3 74.3 - - - -
229 ALA* 1.3 55.2 - - - +
249 ASP* 3.0 10.9 + - - +
289 ARG* 3.5 37.7 - - + -
949 LEU* 4.3 28.9 - - + -
969 VAL* 3.7 26.5 - - + -
1019 HIS* 4.6 7.2 - + - -
3409 TRP* 3.5 1.5 - - - -
641D LYS 5.1 0.4 - - - +
642D LYS* 2.2 46.0 - - - +
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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