Contacts of the strand formed by residues 178 - 182 (chain D) in PDB entry 3PTZ
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 178 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159D ASN* 4.0 10.5 - - - +
162D PHE* 5.1 0.7 - - - -
175D PRO* 3.8 22.0 - - + -
177D ARG* 1.3 80.4 - - - +
179D LEU* 1.3 62.7 + - - +
180D ILE* 4.1 8.1 - - + -
199D TYR* 3.8 42.6 - - + -
203D VAL* 4.2 23.3 - - + -
207D LYS 3.2 5.1 + - - +
208D ILE* 3.7 11.8 - - + +
209D LEU* 2.9 30.1 + - - +
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Residues in contact with LEU 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254C ALA* 4.7 8.7 - - + -
159D ASN* 2.9 20.2 + - - +
160D PRO* 3.2 22.4 + - + +
162D PHE* 3.8 31.1 - - + -
177D ARG* 4.2 3.1 - - + -
178D VAL* 1.3 75.8 - - - +
180D ILE* 1.3 61.1 + - - +
209D LEU* 3.7 26.7 - - + +
211D THR* 3.8 24.9 - - + -
216D SER* 3.3 35.9 - - - +
219D SER* 3.7 17.9 - - - +
220D LYS 4.9 0.9 - - - +
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Residues in contact with ILE 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D LEU* 4.3 13.2 - - + -
158D SER 3.3 6.3 - - - +
159D ASN* 3.6 13.9 - - - +
178D VAL* 4.2 4.7 - - + -
179D LEU* 1.3 78.4 - - - +
181D GLY* 1.3 64.7 + - - +
192D VAL* 4.5 13.4 - - + +
195D LEU* 3.8 38.1 - - + -
196D CYS* 3.9 29.2 - - - +
199D TYR* 4.1 13.7 - - + -
208D ILE* 4.3 7.9 - - + -
209D LEU 3.1 10.2 + - - +
210D THR* 3.2 12.8 - - + -
211D THR* 3.0 23.3 + - - +
216D SER* 4.7 0.2 - - - -
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Residues in contact with GLY 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D LEU* 3.2 7.3 - - - +
158D SER* 2.8 39.6 + - - -
180D ILE* 1.3 74.9 - - - +
182D GLY* 1.3 57.5 + - - -
192D VAL* 4.3 2.7 - - - -
211D THR* 3.0 10.3 - - - -
212D ASN 3.6 19.5 - - - -
213D THR* 4.0 2.8 - - - +
216D SER* 4.0 10.0 + - - -
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Residues in contact with GLY 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D VAL 4.1 0.7 - - - -
157D LEU* 3.8 11.4 - - - -
181D GLY* 1.3 75.0 - - - -
183D ASP* 1.3 70.0 + - - +
184D GLU* 3.4 1.2 + - - +
188D GLY* 4.9 0.4 - - - -
189D GLN* 4.3 4.5 + - - -
192D VAL* 3.7 20.3 - - - +
211D THR 2.9 14.9 + - - +
212D ASN* 3.4 9.1 + - - +
213D THR* 3.7 11.9 - - - -
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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