Contacts of the strand formed by residues 268 - 276 (chain A) in PDB entry 1F1H
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A PRO* 3.8 25.8 - - + -
129A GLU 3.4 4.3 - - - -
130A PRO* 3.8 24.2 - - + -
235A ILE* 4.2 13.7 - - + -
239A LYS* 6.4 0.2 - - - -
267A GLY* 1.3 74.1 - - - +
269A HIS* 1.3 67.5 + - - +
270A CYS* 3.4 5.5 + - - -
321A ARG* 4.4 0.4 - - - +
361A PRO* 2.7 34.4 + - + +
362A ASP 3.6 28.0 - - - +
363A PRO* 3.7 12.1 - - + +
365A ALA* 4.3 18.6 - - + +
367A PRO* 5.2 4.9 - - + -
370A CYS* 4.9 2.0 - - - -
371A PHE* 4.3 20.6 - - + -
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Residues in contact with HIS 269 (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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127A GLY 3.7 0.9 - - - +
128A PRO* 3.1 4.3 - - - +
129A GLU* 2.7 47.5 + - + +
131A GLU* 5.7 6.6 + - - -
267A GLY* 5.2 2.8 - - - -
268A MET* 1.3 75.5 - - - +
270A CYS* 1.3 58.4 + - - +
271A HIS 4.0 0.4 - - - -
321A ARG* 4.5 9.2 + - - -
329A PRO* 5.6 1.0 - - - +
357A GLU* 3.0 16.4 + - + +
358A VAL 3.5 6.3 - - - +
359A ARG* 3.4 61.3 + - + +
470A MN 2.3 32.5 + - - -
1471A ADP 4.8 2.2 + - - -
50B ASP* 5.5 4.7 - - - -
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Residues in contact with CYS 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A PHE* 4.7 11.7 - - + -
127A GLY 4.0 2.9 - - - -
128A PRO* 4.4 7.4 - - - -
268A MET* 3.4 17.9 - - - -
269A HIS* 1.3 75.5 - - - +
271A HIS* 1.3 63.2 + - - +
272A MET* 3.7 9.1 + - + +
356A ILE 3.6 1.0 - - - +
357A GLU* 3.4 2.5 - - - -
358A VAL* 2.8 39.8 + - + +
361A PRO* 4.3 14.6 - - - -
370A CYS* 5.0 0.4 - - - -
371A PHE* 4.0 27.4 - - - -
374A LEU* 4.5 17.7 - - + -
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Residues in contact with HIS 271 (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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125A LEU 3.7 0.2 - - - +
126A PHE* 3.5 2.3 - - - -
127A GLY 2.9 43.8 + - - +
129A GLU* 3.1 22.1 + - - -
269A HIS* 5.1 0.2 - - + -
270A CYS* 1.3 73.0 - - - +
272A MET* 1.3 64.1 + - - +
344A ARG* 4.8 2.7 - - - -
346A PRO* 4.1 9.6 - - + +
355A ARG* 2.9 29.1 + - - -
356A ILE 3.2 6.7 - - - +
357A GLU* 3.0 44.0 + - + +
1471A ADP 3.2 49.1 + - + -
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Residues in contact with MET 272 (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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124A VAL* 6.0 1.1 - - + -
125A LEU 3.2 8.7 - - - +
126A PHE* 3.5 42.8 - - + -
270A CYS* 3.9 9.4 - - + +
271A HIS* 1.3 81.2 - - - +
273A SER* 1.3 62.8 + - - +
282A PHE* 4.0 2.7 - - - -
297A TYR* 3.6 27.4 - - + +
301A VAL* 5.2 0.4 - - + -
355A ARG* 3.0 20.8 - - - +
356A ILE* 2.8 35.3 + - + +
358A VAL* 3.2 35.9 - - + -
374A LEU* 3.9 17.3 - - + -
1471A ADP 4.5 1.8 - - - -
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Residues in contact with SER 273 (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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124A VAL* 3.9 3.0 - - - +
125A LEU* 2.9 41.0 + - - +
272A MET* 1.3 79.0 - - - +
274A LEU* 1.3 67.3 + - - +
275A ALA* 5.7 0.2 - - - +
280A ASN* 3.9 12.3 + - - -
282A PHE* 3.8 11.9 - - - -
297A TYR* 6.1 0.4 - - - -
354A ARG 3.7 17.7 - - - -
355A ARG* 3.9 0.7 - - - -
1471A ADP 2.9 29.1 + - - -
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Residues in contact with LEU 274 (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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115A LEU* 3.9 17.3 - - + -
120A ILE* 4.8 3.8 - - + -
121A ALA* 4.0 13.7 - - + -
123A THR 3.7 8.7 - - - +
124A VAL* 3.3 33.0 - - + -
125A LEU* 5.8 0.2 - - - -
273A SER* 1.3 76.9 + - - +
275A ALA* 1.3 63.8 + - - +
280A ASN* 3.4 8.3 - - - +
281A LEU* 3.1 26.5 + - + +
282A PHE* 3.5 30.2 - - + -
293A GLN* 5.1 1.6 - - - +
297A TYR* 3.8 22.7 - - + -
375A LEU* 4.4 3.6 - - + -
379A LEU* 4.3 9.2 - - + -
382A ILE* 4.1 14.6 - - + -
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Residues in contact with ALA 275 (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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121A ALA* 3.2 4.9 - - - +
122A ASP* 2.8 29.6 + - - +
123A THR* 3.1 23.4 + - - +
125A LEU* 5.0 13.9 - - + -
273A SER* 5.7 0.2 - - - +
274A LEU* 1.3 78.7 - - - +
276A LYS* 1.3 62.3 + - - +
278A GLY* 5.2 4.7 - - - +
279A THR 3.2 18.4 - - - +
280A ASN* 4.7 2.0 - - - -
281A LEU* 4.0 2.2 - - - -
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Residues in contact with LYS 276 (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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119A GLY* 2.9 35.9 + - - +
120A ILE 4.6 4.0 - - - +
121A ALA* 4.3 11.4 + - - +
122A ASP* 3.2 16.6 + - - +
275A ALA* 1.3 74.6 - - - +
277A ASN* 1.3 90.4 + - - +
278A GLY 3.2 0.2 - - - -
279A THR* 2.8 25.5 + - - -
281A LEU* 3.5 19.0 - - + +
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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