Contacts of the strand formed by residues 198 - 206 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130C GLU* 3.1 48.8 + - - +
131C ILE* 3.6 2.7 - - - -
132C ASP* 2.7 40.4 + - - +
133C VAL 3.4 6.1 + - - -
196C GLY 4.1 2.5 - - - +
197C SER* 1.3 72.1 - - - +
199C VAL* 1.3 60.2 + - - +
225C ASN* 3.2 31.9 + - - +
227C ALA* 4.1 11.4 - - + +
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Residues in contact with VAL 199 (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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133C VAL* 3.5 11.7 - - + +
135C MET* 3.6 31.2 - - + -
193C MET* 3.9 26.0 - - + -
197C SER* 4.0 14.6 - - - +
198C ASN* 1.3 78.2 - - - +
200C LEU* 1.3 66.8 + - - +
201C ILE* 3.8 2.5 + - + +
219C LEU* 3.7 28.9 - - + -
224C ALA* 4.3 0.2 - - + -
225C ASN 2.8 16.3 + - - +
226C VAL* 3.6 4.0 - - - +
227C ALA* 2.7 30.9 + - - +
228C GLY 3.6 2.9 + - - +
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Residues in contact with LEU 200 (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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122C PHE* 5.0 1.8 - - + +
126C PHE* 3.7 36.6 - - + -
131C ILE* 3.8 27.5 - - + +
133C VAL 3.0 8.6 + - - +
134C VAL* 3.3 11.9 - - + +
135C MET 2.8 26.9 + - - -
148C ALA* 4.9 3.8 - - + -
152C LEU* 3.8 28.7 - - + -
198C ASN 4.1 0.4 + - - -
199C VAL* 1.3 72.1 - - - +
201C ILE* 1.3 65.9 + - - +
202C ILE* 3.9 19.3 - - + -
228C GLY* 3.5 28.3 - - - +
229C ILE 3.9 0.9 - - - +
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Residues in contact with ILE 201 (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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135C MET* 3.5 8.3 - - + -
199C VAL* 4.2 13.9 - - + +
200C LEU* 1.3 75.2 - - - +
202C ILE* 1.3 65.9 + - - +
212C ILE* 4.1 10.1 - - + -
215C MET* 3.6 42.2 - - + -
216C ILE* 4.0 25.6 - - + -
219C LEU* 3.9 22.2 - - + -
226C VAL* 4.2 13.0 - - + -
228C GLY 2.9 11.2 + - - +
229C ILE* 3.3 18.8 - - + -
230C GLY 2.8 26.0 + - - -
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Residues in contact with ILE 202 (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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122C PHE* 3.6 39.7 - - + -
134C VAL* 3.6 24.0 - - + -
135C MET 2.8 13.4 + - - +
136C THR* 2.7 30.8 + - - -
141C GLY 5.0 1.1 - - - +
144C LEU* 4.0 24.7 - - + -
145C ALA* 4.2 14.8 - - + +
148C ALA* 4.7 2.7 - - + -
200C LEU* 3.9 23.1 - - + -
201C ILE* 1.3 85.7 - - - +
203C ASP* 1.3 65.0 + - - +
215C MET* 4.2 3.6 - - - +
230C GLY 3.3 10.8 - - - +
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Residues in contact with ASP 203 (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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136C THR* 4.3 7.1 + - - -
137C VAL* 5.4 3.3 + - - +
141C GLY* 5.4 1.2 - - - -
144C LEU* 3.9 8.7 - - - +
202C ILE* 1.3 77.6 - - - +
204C ASP* 1.3 64.6 + - - +
205C PHE 3.4 8.2 - - - +
206C MET* 4.4 0.7 + - - -
211C THR* 4.4 4.0 - - - +
212C ILE* 3.9 35.2 - - + +
215C MET* 4.8 8.0 - - - +
230C GLY 3.0 6.5 + - - +
231C VAL* 3.1 12.0 - - + -
232C LEU 3.1 21.3 + - - -
606C PCP 2.5 43.6 + - - -
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Residues in contact with ASP 204 (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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105C LEU* 4.4 6.5 - - + +
109C LEU* 3.9 27.1 - - + +
140C LYS* 4.1 5.0 - - - +
141C GLY* 3.9 19.4 + - - -
144C LEU* 3.8 18.3 - - + +
203C ASP* 1.3 75.0 + - - +
205C PHE* 1.3 74.5 + - - +
231C VAL 5.1 0.2 - - - -
232C LEU* 3.2 7.6 - - - +
233C VAL* 2.9 28.3 + - - +
606C PCP 2.9 46.2 + - - -
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Residues in contact with PHE 205 (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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101C GLY 4.1 12.3 - - - -
102C TYR* 3.3 38.8 - + - -
103C VAL* 4.7 7.4 - - + -
105C LEU* 4.4 11.0 - - + -
203C ASP* 3.6 3.5 - - - -
204C ASP* 1.3 94.7 + - - +
206C MET* 1.3 57.5 + - - +
207C LYS* 3.5 34.8 - - + -
233C VAL* 3.2 30.3 - - + -
235C ALA* 4.1 17.9 - - + -
252C LEU* 3.9 20.9 - - + -
606C PCP 2.9 32.0 + + - +
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Residues in contact with MET 206 (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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203C ASP* 4.4 1.3 - - - -
204C ASP 4.3 0.2 - - - -
205C PHE* 1.3 72.1 - - - +
207C LYS* 1.3 61.0 + - - +
209C GLY* 3.9 27.8 - - - +
212C ILE* 3.7 28.7 - - + -
231C VAL* 4.4 9.7 - - + +
233C VAL 2.9 12.0 + - - +
234C GLU* 3.6 13.6 - - + -
235C ALA 2.9 27.3 + - - -
238C VAL* 3.6 17.4 - - + +
243C VAL* 4.6 14.1 - - - -
246C TYR* 3.3 48.9 - - + +
606C PCP 3.5 4.9 - - - +
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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