Contacts of the strand formed by residues 268 - 276 (chain J) 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 MET 268 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128J PRO* 3.8 21.3 - - + -
129J GLU 3.2 3.8 - - - +
130J PRO* 3.7 23.1 - - + -
235J ILE* 3.4 48.9 - - + -
239J LYS* 6.1 1.1 - - + -
267J GLY* 1.3 73.7 - - - -
269J HIS* 1.3 63.9 + - - +
270J CYS* 3.7 3.9 - - - -
321J ARG* 4.5 0.2 - - - +
361J PRO* 2.9 35.6 + - - +
362J ASP 3.7 15.5 - - - +
363J PRO* 3.2 25.2 - - + +
365J ALA* 5.3 7.6 - - - +
367J PRO* 5.4 2.9 - - + -
370J CYS* 6.0 1.1 - - - -
371J PHE* 4.9 12.3 - - + -
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Residues in contact with HIS 269 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127J GLY 3.7 1.6 - - - +
128J PRO* 3.1 6.8 - - - +
129J GLU* 2.9 45.7 + - + +
131J GLU* 4.8 3.8 - - - -
220J GLU* 5.9 0.4 - - - -
267J GLY 4.6 1.9 - - - -
268J MET* 1.3 74.9 - - - +
270J CYS* 1.3 59.2 + - - +
271J HIS* 4.1 0.9 - - - -
321J ARG* 4.5 0.9 - - - -
357J GLU* 3.3 16.1 + - + +
358J VAL 3.6 6.3 - - - -
359J ARG* 3.2 43.5 + - + +
470J MN 2.4 24.0 + - - -
5909J PPQ 2.9 65.6 + - + +
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Residues in contact with CYS 270 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126J PHE* 4.7 8.1 - - + -
127J GLY 3.9 1.3 - - - -
128J PRO* 4.3 9.4 - - - -
268J MET* 3.7 12.8 - - - -
269J HIS* 1.3 79.2 - - - +
271J HIS* 1.3 64.6 + - - +
272J MET* 3.6 12.2 - - + +
357J GLU* 3.3 1.0 - - - -
358J VAL* 2.7 41.6 + - + +
361J PRO* 4.4 7.9 - - + -
370J CYS* 5.1 0.9 - - - -
371J PHE* 4.1 26.5 - - - -
374J LEU* 4.3 24.7 - - + -
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Residues in contact with HIS 271 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126J PHE* 3.3 3.1 - - - +
127J GLY 2.9 42.2 + - - +
129J GLU* 3.4 17.2 + - - -
270J CYS* 1.3 74.7 - - - +
272J MET* 1.3 66.4 + - - +
344J ARG* 5.2 1.1 - - - -
346J PRO* 5.0 5.8 - - + -
355J ARG* 3.0 29.9 + - - -
356J ILE 3.1 3.4 - - - -
357J GLU* 2.7 51.9 + - + +
4480J ADP 2.7 53.0 + - + -
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Residues in contact with MET 272 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124J VAL* 5.4 1.3 - - + -
125J LEU 3.0 13.2 - - - +
126J PHE* 3.5 40.2 - - + -
270J CYS* 3.6 11.2 + - + +
271J HIS* 1.3 78.8 - - - +
273J SER* 1.3 62.1 + - - +
282J PHE* 4.0 0.8 - - - -
297J TYR* 3.7 25.8 - - + +
301J VAL* 5.4 0.2 - - + -
355J ARG* 3.0 7.0 - - - +
356J ILE* 2.8 50.8 + - + +
358J VAL* 3.2 36.3 - - + -
374J LEU* 3.8 17.0 - - + -
4480J ADP 4.4 2.2 + - - -
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Residues in contact with SER 273 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123J THR 4.4 0.2 - - - +
124J VAL* 3.9 1.7 - - - +
125J LEU* 2.9 36.2 + - - +
272J MET* 1.3 80.7 - - - +
274J LEU* 1.3 65.9 + - - +
280J ASN* 4.1 10.3 + - - -
282J PHE* 3.7 14.6 - - - -
297J TYR* 6.0 0.4 - - - -
354J ARG 3.7 16.6 - - - -
355J ARG* 3.8 0.9 - - - -
4480J ADP 2.5 32.6 + - - -
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Residues in contact with LEU 274 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115J LEU* 3.8 19.3 - - + -
120J ILE* 5.0 2.9 - - + -
121J ALA* 3.9 13.0 - - + -
123J THR 3.5 15.5 - - - +
124J VAL* 3.6 26.5 - - + -
273J SER* 1.3 76.9 - - - +
275J ALA* 1.3 62.1 + - - +
280J ASN* 3.4 8.1 - - - +
281J LEU* 3.1 28.8 + - + +
282J PHE* 3.3 25.8 - - + -
293J GLN* 5.4 1.6 - - + -
297J TYR* 3.7 28.7 - - + -
375J LEU* 4.4 1.6 - - + -
379J LEU* 4.3 15.3 - - + -
382J ILE* 4.4 9.2 - - + -
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Residues in contact with ALA 275 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121J ALA* 3.2 5.4 - - - +
122J ASP* 2.8 33.7 + - - +
123J THR* 3.0 25.1 + - - +
125J LEU* 4.8 15.0 - - + -
274J LEU* 1.3 76.8 - - - +
276J LYS* 1.3 55.2 + - - +
278J GLY* 5.4 4.5 - - - +
279J THR 3.3 17.0 - - - +
280J ASN* 4.9 2.0 - - + -
281J LEU* 3.7 3.6 - - - -
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Residues in contact with LYS 276 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119J GLY* 3.0 30.9 + - - -
120J ILE 4.2 13.7 - - - +
121J ALA* 4.4 6.4 - - - +
122J ASP* 3.2 18.4 + - - +
275J ALA* 1.3 78.2 - - - +
277J ASN* 1.3 93.1 + - - +
279J THR* 3.0 20.8 + - - -
281J LEU* 3.4 18.6 - - + +
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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