Contacts of the strand formed by residues 198 - 206 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A GLU* 3.1 41.8 + - - +
131A ILE* 3.6 2.8 - - - -
132A ASP* 2.8 51.6 + - - +
133A VAL* 3.4 7.0 + - - +
196A GLY 4.6 3.8 + - - -
197A SER* 1.3 70.5 - - - +
199A VAL* 1.3 60.6 + - - +
225A ASN* 3.3 31.2 + - - +
227A ALA* 4.2 6.4 - - + +
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Residues in contact with VAL 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A VAL* 3.5 22.7 - - + +
135A MET* 3.6 31.0 - - + -
193A MET* 4.3 3.1 - - + -
197A SER* 3.7 16.8 - - - +
198A ASN* 1.3 77.1 - - - +
200A LEU* 1.3 66.4 + - - +
201A ILE* 3.7 3.4 + - + -
219A LEU* 3.7 37.2 - - + -
224A ALA* 4.0 3.4 - - + -
225A ASN 2.8 15.4 + - - +
226A VAL* 3.6 3.6 - - - +
227A ALA* 2.8 27.9 + - - +
228A GLY 3.5 4.5 + - - +
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Residues in contact with LEU 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A PHE* 5.0 1.1 - - + +
126A PHE* 3.5 42.0 - - + -
131A ILE* 4.1 21.9 - - + +
133A VAL 2.9 12.6 + - - +
134A VAL* 3.2 14.6 - - + +
135A MET 2.9 23.9 + - - -
148A ALA* 5.0 3.4 - - + -
152A LEU* 4.1 25.8 - - + -
198A ASN 4.1 0.4 + - - -
199A VAL* 1.3 73.0 - - - +
201A ILE* 1.3 64.7 + - - +
202A ILE* 3.8 19.3 - - + -
228A GLY* 3.5 26.7 - - - +
229A ILE 3.9 0.9 - - - +
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Residues in contact with ILE 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A MET* 3.4 11.4 - - + -
199A VAL* 3.7 16.6 + - + +
200A LEU* 1.3 73.6 - - - +
202A ILE* 1.3 66.5 + - - +
212A ILE* 4.3 14.8 - - + +
215A MET* 3.7 43.5 - - + -
216A ILE* 4.0 24.2 - - + -
219A LEU* 3.9 21.1 - - + -
226A VAL* 4.5 8.7 - - + -
228A GLY 3.0 11.6 + - - +
229A ILE* 3.3 12.6 - - + +
230A GLY 2.9 26.0 + - - +
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Residues in contact with ILE 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A PHE* 3.5 41.5 - - + -
134A VAL* 3.7 21.5 - - + -
135A MET 2.9 10.4 + - - +
136A THR* 2.7 30.7 + - - -
141A GLY 4.9 1.8 - - - +
144A LEU* 4.0 21.5 - - + -
145A ALA* 4.0 20.0 - - + +
148A ALA* 4.5 7.2 - - + -
200A LEU* 3.8 24.5 - - + -
201A ILE* 1.3 85.8 - - - +
203A ASP* 1.3 62.8 + - - +
215A MET* 4.7 1.4 - - - +
230A GLY* 3.3 8.5 - - - +
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Residues in contact with ASP 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A THR* 4.5 5.2 + - - -
137A VAL* 5.4 4.9 + - - +
141A GLY* 5.6 0.7 - - - -
144A LEU* 4.2 8.3 - - - +
201A ILE* 5.3 0.2 - - + -
202A ILE* 1.3 77.6 - - - +
204A ASP* 1.3 63.4 + - - +
205A PHE 3.5 8.4 - - - +
206A MET* 4.0 1.0 - - - -
211A THR* 5.0 1.3 - - - +
212A ILE* 3.7 35.4 - - + +
215A MET* 4.7 9.8 - - + +
230A GLY 2.9 6.1 + - - +
231A VAL* 3.0 31.5 - - + -
232A LEU 3.1 3.5 + - - -
604A PCP 2.7 45.0 + - - -
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Residues in contact with ASP 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A LEU* 5.3 1.3 - - + +
109A LEU* 3.3 33.3 - - + +
140A LYS* 3.2 24.8 - - - +
141A GLY* 3.2 18.6 + - - -
144A LEU* 4.4 4.2 - - + +
203A ASP* 1.3 75.3 + - - +
205A PHE* 1.3 81.2 + - + +
206A MET 4.2 0.2 - - - -
231A VAL* 5.1 0.2 - - - -
232A LEU* 3.5 10.4 - - - +
233A VAL* 3.0 29.8 + - - +
604A PCP 2.9 34.2 + - - -
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Residues in contact with PHE 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A VAL* 5.3 7.9 - - + -
105A LEU* 3.5 32.3 - - + -
140A LYS* 6.2 2.0 - - - -
203A ASP* 3.6 2.6 - - - -
204A ASP* 1.3 94.1 + - - +
206A MET* 1.3 66.3 + - - +
207A LYS* 4.5 4.7 - - + -
233A VAL* 3.2 20.9 - - + -
234A GLU 4.3 0.2 - - - -
235A ALA* 4.0 26.7 - - + -
252A LEU* 3.6 29.2 - - + -
604A PCP 2.7 40.1 + + + +
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Residues in contact with MET 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A ASP* 4.0 3.1 + - - +
205A PHE* 1.3 73.8 - - - +
207A LYS* 1.3 61.0 + - - +
209A GLY* 4.2 9.6 - - - -
212A ILE* 3.4 25.4 - - + -
231A VAL* 3.9 19.4 - - + +
233A VAL 2.9 12.3 + - - +
234A GLU* 3.5 11.5 - - + +
235A ALA* 2.9 27.7 + - - +
238A VAL* 4.8 10.0 - - + +
242A LEU* 3.7 28.5 - - - -
246A TYR* 3.4 40.2 - - + -
604A PCP 3.7 15.9 - - - +
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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