Contacts of the strand formed by residues 183 - 189 (chain D) in PDB entry 1P4A
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 ILE 183 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174D ASN* 3.7 35.4 - - + +
175D TYR 3.7 9.2 - - - +
176D VAL* 4.3 10.1 - - + -
181D ASN 4.8 3.4 - - - +
182D ARG* 1.3 76.1 - - - +
184D GLN* 1.3 65.6 + - - +
185D THR* 5.1 3.8 - - + +
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Residues in contact with GLN 184 (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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161D LYS* 4.0 23.7 + - + +
174D ASN* 3.4 4.0 - - - -
175D TYR* 2.9 56.9 + - + +
177D SER* 3.4 33.3 - - - +
179D SER* 5.7 2.6 - - - -
180D SER* 5.3 7.2 - - - -
182D ARG* 3.4 9.6 + - + +
183D ILE* 1.3 78.1 - - - +
185D THR* 1.3 64.8 + - - +
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Residues in contact with THR 185 (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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160D ARG 3.8 0.2 - - - +
161D LYS* 3.2 31.5 + - - +
162D ASP* 4.7 11.6 + - - +
172D SER* 5.3 7.0 + - - -
173D ILE 3.3 8.1 - - - -
174D ASN* 3.2 24.7 - - - +
175D TYR* 3.8 2.9 - - - -
183D ILE* 5.1 3.8 - - + +
184D GLN* 1.3 79.2 - - - +
186D MET* 1.3 62.6 + - - +
187D SER* 5.6 1.4 - - - -
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Residues in contact with MET 186 (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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137D VAL* 4.8 6.3 - - + -
159D VAL* 3.4 18.8 - - + -
160D ARG 3.0 7.4 - - - +
161D LYS* 4.9 2.2 - - + -
171D VAL 4.0 0.2 - - - +
172D SER* 3.4 2.3 - - - -
173D ILE* 2.9 44.2 + - + +
175D TYR* 3.6 40.8 - - + +
185D THR* 1.3 74.8 - - - +
187D SER* 1.3 62.7 + - - +
211D THR* 3.4 31.6 - - + +
214D GLY 3.5 23.8 - - - +
215D MET* 3.5 17.9 - - + +
218D LEU* 4.5 5.6 - - + +
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Residues in contact with SER 187 (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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159D VAL* 3.6 5.7 - - - +
160D ARG* 2.7 46.8 + - - +
162D ASP* 4.0 14.8 + - - -
170D THR* 3.8 13.2 - - - +
171D VAL 3.1 7.6 - - - -
172D SER* 3.3 22.2 - - - -
185D THR* 5.6 1.6 - - - -
186D MET* 1.3 76.4 - - - +
188D LEU* 1.3 63.2 + - - +
218D LEU* 4.6 2.2 - - - -
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Residues in contact with LEU 188 (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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135D MET* 3.8 28.7 - - + -
157D VAL* 3.7 19.5 - - + -
158D ILE 3.5 27.4 - - - +
159D VAL* 4.2 2.7 - - - -
160D ARG* 5.8 2.2 - - + -
170D THR* 4.0 3.1 - - - -
171D VAL* 2.8 32.9 + - - +
187D SER* 1.3 77.0 - - - +
189D ALA* 1.3 71.6 + - - +
190D LYS 3.5 0.3 + - - -
192D SER* 4.1 14.4 - - - +
193D MET* 4.1 13.0 - - + -
218D LEU* 4.0 14.8 - - + +
222D PHE* 4.1 21.7 - - + -
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Residues in contact with ALA 189 (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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104C TYR* 6.1 0.9 - - + -
169D SER 3.5 10.8 - - - +
170D THR* 3.8 13.4 - - - +
188D LEU* 1.3 80.8 - - - +
190D LYS* 1.3 64.5 + - - +
191D ARG* 4.1 14.8 - - + +
192D SER* 3.0 32.9 + - - +
193D MET 4.0 1.4 + - - -
222D PHE* 4.2 1.4 - - - -
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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