Contacts of the strand formed by residues 198 - 206 (chain B) 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 ASN 198 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130B GLU* 3.1 45.6 - - - +
131B ILE* 3.6 1.7 - - - -
132B ASP* 2.6 50.7 + - - +
133B VAL 3.4 6.9 + - - +
196B GLY 4.4 3.4 + - - -
197B SER* 1.3 70.7 - - - +
199B VAL* 1.3 59.2 + - - +
225B ASN* 3.1 32.0 + - - +
227B ALA* 4.0 7.7 - - + +
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Residues in contact with VAL 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B VAL* 3.5 13.9 - - + -
135B MET* 3.6 30.7 - - + -
193B MET* 3.6 30.1 - - - -
197B SER* 3.8 13.7 - - - +
198B ASN* 1.3 75.8 - - - +
200B LEU* 1.3 66.9 + - - +
201B ILE* 3.7 3.7 + - + +
219B LEU* 3.8 26.7 - - + -
224B ALA* 4.2 1.1 - - + -
225B ASN 2.8 15.7 + - - +
226B VAL* 3.7 4.9 - - - +
227B ALA* 2.9 27.2 + - - +
228B GLY 3.6 4.2 + - - +
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Residues in contact with LEU 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B PHE* 5.1 1.3 - - + +
126B PHE* 3.8 34.8 - - + -
131B ILE* 3.9 34.6 - - + +
133B VAL 3.0 8.5 + - - +
134B VAL* 3.3 12.7 - - + +
135B MET 2.8 27.1 + - - -
148B ALA* 5.0 2.7 - - + -
152B LEU* 3.9 20.2 - - + -
198B ASN 4.1 0.6 + - - -
199B VAL* 1.3 71.8 - - - +
201B ILE* 1.3 68.2 + - - +
202B ILE* 3.7 19.4 + - + -
227B ALA* 5.0 0.2 - - - -
228B GLY* 3.4 30.3 - - - +
229B ILE 3.8 0.2 - - - +
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Residues in contact with ILE 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B MET* 3.4 8.3 - - - +
199B VAL* 4.2 17.0 - - + +
200B LEU* 1.3 75.8 - - - +
202B ILE* 1.3 64.8 + - - +
212B ILE* 4.2 17.3 - - + +
215B MET* 3.7 50.7 - - + -
216B ILE* 4.1 21.8 - - + +
219B LEU* 3.9 18.8 - - + -
226B VAL* 4.6 8.1 - - + -
228B GLY 2.9 12.8 + - - +
229B ILE* 3.3 11.1 - - + +
230B GLY 2.8 25.7 + - - -
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Residues in contact with ILE 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B PHE* 3.8 33.0 - - + -
134B VAL* 3.8 21.1 - - + -
135B MET 2.9 7.2 + - - +
136B THR* 2.8 25.5 + - - -
141B GLY 4.7 0.4 - - - +
144B LEU* 3.8 29.4 - - + -
145B ALA* 4.0 16.4 - - + +
148B ALA* 4.4 6.5 - - + -
200B LEU* 3.9 22.0 - - + -
201B ILE* 1.3 86.6 - - - +
203B ASP* 1.3 68.3 + - - +
215B MET* 4.6 0.3 - - - +
230B GLY* 3.1 18.6 - - - +
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Residues in contact with ASP 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B THR* 3.5 7.0 + - - -
137B VAL* 3.9 10.6 - - - +
141B GLY* 3.5 14.4 - - - -
144B LEU* 4.0 9.0 - - - +
202B ILE* 1.3 78.1 - - - +
204B ASP* 1.3 75.4 + - - +
205B PHE 4.5 4.3 - - - +
211B THR* 4.0 4.3 - - - +
212B ILE* 4.3 24.0 - - + +
215B MET* 4.2 4.4 - - + +
230B GLY 2.9 7.9 + - - -
231B VAL* 3.0 26.8 - - + +
232B LEU 3.1 3.3 + - - -
605B PCP 2.2 43.4 + - - -
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Residues in contact with ASP 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B LEU* 4.0 14.9 - - + +
109B LEU* 4.1 14.7 - - + +
140B LYS* 3.5 30.6 - - - +
141B GLY* 3.8 1.4 + - - -
144B LEU* 3.5 23.6 - - + +
203B ASP* 1.3 79.6 + - - +
205B PHE* 1.3 77.9 + - - +
231B VAL* 4.8 0.2 - - - -
232B LEU* 3.2 8.1 - - + +
233B VAL* 2.9 26.6 + - - +
605B PCP 2.9 30.2 + - - +
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Residues in contact with PHE 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B GLY 3.9 16.2 - - - -
102B TYR* 3.5 44.0 - + - -
103B VAL* 4.7 8.5 - - + -
105B LEU* 4.3 11.0 - - + -
203B ASP* 3.6 3.9 - - - +
204B ASP* 1.3 95.8 - - - +
206B MET* 1.3 60.1 + - - +
207B LYS* 3.8 25.4 - - + -
231B VAL* 5.2 0.7 - - - -
233B VAL* 3.2 35.4 - - + -
235B ALA* 4.0 17.0 - - + -
252B LEU* 4.0 14.6 - - + -
605B PCP 3.2 34.4 + + + +
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Residues in contact with MET 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B PHE* 1.3 72.3 - - - +
207B LYS* 1.3 61.3 + - - +
209B GLY* 3.9 12.8 - - - -
212B ILE* 3.9 19.5 - - + -
231B VAL* 4.2 16.5 - - + +
233B VAL 2.8 12.9 + - - +
234B GLU* 3.4 11.9 - - + +
235B ALA 2.9 27.2 + - - -
238B VAL* 3.8 26.0 - - + +
243B VAL* 3.8 31.0 - - - -
246B TYR* 3.7 42.4 - - + -
605B PCP 3.5 4.3 - - - +
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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