Contacts of the strand formed by residues 268 - 276 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128E PRO* 3.8 26.2 - - + -
129E GLU 3.4 4.3 - - - -
130E PRO* 3.8 24.7 - - + -
235E ILE* 4.2 13.5 - - + -
239E LYS* 6.4 0.7 - - - -
267E GLY* 1.3 74.7 - - - +
269E HIS* 1.3 67.0 + - - +
270E CYS* 3.4 5.9 + - - -
321E ARG* 4.4 0.4 - - - +
361E PRO* 2.7 34.4 + - + +
362E ASP 3.6 28.5 - - - +
363E PRO* 3.7 12.1 - - + +
365E ALA* 4.3 18.2 - - + +
367E PRO* 5.2 4.5 - - + -
370E CYS* 4.9 2.2 - - - -
371E PHE* 4.3 20.6 - - + -
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Residues in contact with HIS 269 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127E GLY 3.7 0.9 - - - +
128E PRO* 3.1 4.5 - - - +
129E GLU* 2.7 47.1 + - + +
131E GLU* 5.7 7.3 + - - -
267E GLY* 3.9 2.8 - - - -
268E MET* 1.3 77.0 - - - +
270E CYS* 1.3 58.7 + - - +
271E HIS 4.0 0.2 - - - -
321E ARG* 4.5 9.3 + - - -
329E PRO* 5.6 1.2 - - - +
357E GLU* 3.0 16.2 + - + +
358E VAL 3.5 7.0 - - - +
359E ARG* 3.4 62.8 + - + +
470E MN 2.3 31.8 + - - -
1475E ADP 4.8 2.4 + - - -
50F ASP* 5.8 4.0 - - - -
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Residues in contact with CYS 270 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126E PHE* 4.7 11.2 - - + -
127E GLY 4.0 2.7 - - - -
128E PRO* 4.4 7.6 - - - -
268E MET* 3.4 18.4 - - - -
269E HIS* 1.3 75.2 - - - +
271E HIS* 1.3 62.1 + - - +
272E MET* 3.7 8.9 + - + +
356E ILE 3.6 1.4 - - - +
357E GLU* 3.4 2.1 - - - -
358E VAL* 2.8 40.1 + - + +
361E PRO* 4.3 14.1 - - + -
370E CYS* 5.0 0.7 - - - -
371E PHE* 4.0 27.6 - - - -
374E LEU* 4.5 17.3 - - + -
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Residues in contact with HIS 271 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125E LEU 3.7 0.2 - - - +
126E PHE* 3.5 1.7 - - - -
127E GLY 2.9 45.7 + - - +
129E GLU* 3.1 22.0 + - - -
269E HIS* 5.1 0.2 - - + -
270E CYS* 1.3 72.8 - - - +
272E MET* 1.3 64.8 + - - +
344E ARG* 4.8 3.8 - - - -
346E PRO* 4.1 9.6 - - + +
355E ARG* 2.9 29.2 + - - -
356E ILE 3.2 6.3 - - - +
357E GLU* 3.0 41.5 + - + +
1475E ADP 3.2 48.1 + - + +
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Residues in contact with MET 272 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124E VAL* 6.0 1.1 - - + -
125E LEU 3.2 7.6 - - - +
126E PHE* 3.5 42.4 - - + -
270E CYS* 3.9 10.1 - - + +
271E HIS* 1.3 80.5 - - - +
273E SER* 1.3 61.8 + - - +
282E PHE* 4.0 2.5 - - - -
297E TYR* 3.6 27.4 - - + +
301E VAL* 5.2 0.4 - - + -
355E ARG* 3.0 20.9 - - - +
356E ILE* 2.8 34.1 + - + +
358E VAL* 3.2 35.7 - - + -
374E LEU* 3.9 18.8 - - + -
1475E ADP 4.5 2.2 + - - -
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Residues in contact with SER 273 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124E VAL* 3.9 2.6 - - - +
125E LEU* 2.9 40.5 + - - +
272E MET* 1.3 79.7 - - - +
274E LEU* 1.3 67.2 + - - +
275E ALA* 5.7 0.2 - - - +
280E ASN* 3.9 12.3 + - - -
282E PHE* 3.8 12.1 - - - -
297E TYR* 6.2 0.4 - - - -
354E ARG 3.7 18.4 - - - -
355E ARG* 3.9 0.7 - - - -
1475E ADP 2.9 28.3 + - - -
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Residues in contact with LEU 274 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115E LEU* 3.9 16.6 - - + -
120E ILE* 4.8 3.4 - - + -
121E ALA* 4.0 13.7 - - + -
123E THR 3.7 9.2 - - - +
124E VAL* 3.3 33.2 - - + -
125E LEU* 5.8 0.4 - - - -
273E SER* 1.3 77.1 + - - +
275E ALA* 1.3 63.5 + - - +
280E ASN* 3.4 7.6 - - - +
281E LEU* 3.1 26.8 + - + +
282E PHE* 3.5 29.3 - - + -
293E GLN* 5.1 2.2 - - - +
297E TYR* 3.8 22.7 - - + -
375E LEU* 4.4 4.0 - - + -
379E LEU* 4.3 10.1 - - + -
382E ILE* 4.1 14.8 - - + -
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Residues in contact with ALA 275 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121E ALA* 3.2 4.5 - - - +
122E ASP* 2.8 30.2 + - - +
123E THR* 3.1 23.7 + - - +
125E LEU* 5.0 13.7 - - + -
274E LEU* 1.3 79.1 - - - +
276E LYS* 1.3 61.1 + - - +
278E GLY* 5.2 4.5 - - - +
279E THR 3.2 19.1 - - - +
280E ASN* 4.7 2.2 - - - -
281E LEU* 4.0 2.5 - - - -
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Residues in contact with LYS 276 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119E GLY* 2.9 36.1 + - - +
120E ILE 4.6 4.0 - - - +
121E ALA* 4.3 11.4 - - - +
122E ASP* 3.2 17.0 + - - +
275E ALA* 1.3 75.1 - - - +
277E ASN* 1.3 87.0 + - - +
278E GLY 3.2 0.7 - - - -
279E THR* 2.8 26.1 + - - -
281E LEU* 3.5 18.8 - - + +
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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