Contacts of the strand formed by residues 123 - 135 (chain K) in PDB entry 1FPY
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 THR 123 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112K GLU* 4.9 4.3 - - - +
115K LEU* 3.7 5.1 - - - +
116K ARG* 4.7 7.2 - - - +
121K ALA 3.7 1.2 - - - -
122K ASP* 1.3 99.2 + - + +
124K VAL* 1.3 65.7 + - - +
125K LEU* 4.8 9.8 - - - +
227K THR* 5.0 16.2 - - + -
274K LEU* 3.5 5.2 - - - +
275K ALA* 3.0 40.8 + - - +
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Residues in contact with VAL 124 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112K GLU* 4.0 20.6 + - + +
115K LEU* 3.8 29.4 - - + -
123K THR* 1.3 71.4 - - - +
125K LEU* 1.3 76.6 + - - +
126K PHE* 3.5 24.0 - - + -
227K THR* 3.3 2.9 - - - -
228K MET* 3.0 32.0 + - + -
272K MET* 5.4 1.3 - - + -
273K SER 4.3 2.5 - - - +
274K LEU* 3.6 16.8 - - + -
297K TYR* 4.3 5.6 - - - +
375K LEU* 3.8 24.2 - - + -
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Residues in contact with LEU 125 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123K THR* 4.8 9.9 - - - +
124K VAL* 1.3 89.6 - - - +
126K PHE* 1.3 61.7 + - - +
225K PHE* 3.5 30.5 - - + -
226K ASN 3.9 11.0 - - - +
227K THR* 4.0 10.3 - - + +
271K HIS 4.1 0.2 - - - -
272K MET* 3.0 32.4 - - - +
273K SER* 2.9 35.1 + - - +
275K ALA* 4.8 17.0 - - + -
4481K ADP 4.0 14.6 - - + +
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Residues in contact with PHE 126 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124K VAL* 3.5 18.6 - - + -
125K LEU* 1.3 78.3 - - - +
127K GLY* 1.3 58.6 + - - +
128K PRO* 3.8 2.9 - - + -
225K PHE* 3.1 22.8 - - - -
226K ASN 3.1 16.9 + - - +
228K MET* 3.4 36.3 - - + -
231K LYS* 3.5 21.0 - - + +
270K CYS* 4.7 6.7 - - - -
271K HIS 3.3 3.1 - - - -
272K MET* 3.5 34.8 - - + -
371K PHE* 3.3 59.9 - + + -
374K LEU* 4.0 9.4 - - + -
375K LEU* 4.4 3.6 - - + -
4481K ADP 4.4 0.2 - - - -
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Residues in contact with GLY 127 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126K PHE* 1.3 75.5 - - - +
128K PRO* 1.3 63.1 - - - +
129K GLU* 4.7 0.3 - - - +
225K PHE* 3.9 9.2 - - - -
269K HIS 3.7 1.4 - - - +
270K CYS* 4.7 0.4 - - - -
271K HIS* 2.9 44.3 + - - +
4481K ADP 3.2 28.0 + - - +
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Residues in contact with PRO 128 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126K PHE* 4.5 2.0 - - + -
127K GLY* 1.3 89.1 - - - +
129K GLU* 1.3 63.6 + - - +
130K PRO* 3.2 10.1 - - - +
222K ALA* 5.6 0.5 - - - -
223K THR* 4.3 12.5 + - - +
231K LYS* 3.3 33.9 - - + -
235K ILE* 4.2 6.3 - - + -
268K MET* 3.8 28.5 - - + -
269K HIS 3.1 8.1 - - - +
270K CYS* 4.3 7.9 - - - -
371K PHE* 3.6 26.5 - - + -
4481K ADP 4.3 4.5 + - - -
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Residues in contact with GLU 129 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127K GLY 4.7 2.5 - - - +
128K PRO* 1.3 73.8 - - + +
130K PRO* 1.3 58.2 - - - +
131K GLU* 3.4 2.9 + - - +
220K GLU* 3.5 19.3 - - - +
221K VAL 5.6 0.2 - - - -
222K ALA* 5.8 3.4 - - + +
267K GLY 2.8 26.3 - - - +
268K MET* 3.2 7.3 - - - -
269K HIS* 2.9 23.3 + - + +
271K HIS* 3.4 13.9 + - - -
357K GLU* 2.8 6.4 - - - +
470K MN 1.9 34.2 + - - -
4481K ADP 2.6 54.4 + - - +
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Residues in contact with PRO 130 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128K PRO 3.2 10.5 - - - +
129K GLU* 1.3 80.8 - - - +
131K GLU* 1.3 63.7 + - - +
132K PHE* 3.9 1.2 - - - -
220K GLU* 4.0 4.7 - - + +
221K VAL 4.1 16.2 - - - +
223K THR* 5.0 2.2 - - - +
235K ILE* 3.9 15.5 - - + -
238K TYR* 2.9 47.5 + - + -
239K LYS* 6.2 0.9 - - + -
255K PHE* 4.8 6.3 - - + -
267K GLY 3.9 2.5 - - - +
268K MET* 3.7 36.3 - - + -
363K PRO* 4.7 4.0 - - + -
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Residues in contact with GLU 131 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129K GLU 4.4 0.9 - - - +
130K PRO* 1.3 73.4 - - - +
132K PHE* 1.3 65.6 + - - +
212K GLU* 3.1 16.6 - - + +
218K GLN* 4.8 3.1 - - - +
219K ASN 3.8 4.5 - - - +
220K GLU* 3.0 25.4 - - + +
255K PHE* 3.4 14.9 - - - -
266K SER* 3.7 16.3 - - - -
267K GLY 3.0 28.6 + - - +
269K HIS* 4.8 1.7 - - - -
363K PRO* 3.5 11.8 - - - +
469K MN 2.3 30.0 + - - -
5910K PPQ 2.4 42.5 + - - +
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Residues in contact with PHE 132 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130K PRO 3.9 3.6 - - - -
131K GLU* 1.3 80.6 - - - +
133K PHE* 1.3 75.3 + - - +
134K LEU* 3.9 17.9 - - + -
192K ARG* 5.5 0.9 - - + -
195K MET* 4.0 20.4 - - - -
218K GLN* 3.2 6.1 - - - +
219K ASN* 2.7 68.9 + - + -
220K GLU* 4.2 2.2 - - - -
221K VAL* 4.3 8.1 - - + -
238K TYR* 3.5 19.1 - + - -
242K VAL* 3.9 26.0 - - + -
254K THR 3.5 17.0 - - - +
255K PHE* 3.7 25.8 - + + -
266K SER* 4.0 5.6 - - - -
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Residues in contact with PHE 133 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132K PHE* 1.3 77.2 - - - +
134K LEU* 1.3 65.6 + - - +
135K PHE* 3.3 22.2 - + + -
214K ALA* 3.6 9.0 - - + -
215K THR 3.6 2.7 - - - -
216K ALA 3.5 17.9 - - - -
217K GLY 3.3 4.0 - - - -
218K GLN* 3.4 33.0 - - + -
252K THR 3.9 0.3 - - - +
253K ALA* 3.3 7.3 - - - +
254K THR* 3.2 31.2 + - + -
256K MET 4.9 0.9 - - - -
259K PRO* 3.3 26.9 - - + -
260K MET* 3.1 30.7 - - + -
264K ASN 3.4 21.8 - - - -
266K SER* 3.3 25.1 - - - -
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Residues in contact with LEU 134 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132K PHE* 3.9 21.3 - - + -
133K PHE* 1.3 76.1 - - - +
135K PHE* 1.3 62.9 + - - +
153K ASP* 3.1 23.0 - - - +
188K ALA* 4.9 4.3 - - + -
191K ILE* 4.4 27.6 - - + -
192K ARG* 5.6 1.3 - - + -
195K MET* 4.5 7.4 - - + -
216K ALA 3.6 7.0 + - - +
217K GLY* 2.8 17.1 + - - +
219K ASN* 4.2 14.4 - - - +
246K ALA* 3.8 16.8 - - + -
251K LYS* 4.0 20.8 + - + -
252K THR 3.8 1.3 - - - +
253K ALA* 3.5 31.9 - - + +
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Residues in contact with PHE 135 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462E PHE* 6.3 0.2 - + - -
466E TYR* 3.8 23.3 - + - -
133K PHE* 3.3 27.6 - + + -
134K LEU* 1.3 72.9 - - - +
136K ASP* 1.3 62.3 + - - +
137K ASP 4.1 6.3 - - - +
138K ILE* 5.0 2.9 - - + -
151K ILE* 3.6 32.8 - - + -
152K ASP 3.4 7.6 - - - +
153K ASP* 3.3 15.7 - - + -
216K ALA* 3.2 32.5 - - + -
251K LYS* 3.5 9.9 - - - +
252K THR* 3.0 39.0 + - + -
254K THR* 3.4 25.1 - - + -
259K PRO* 4.2 17.0 - - + -
260K MET* 4.2 3.6 - - + -
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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