Contacts of the strand formed by residues 268 - 276 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128K PRO* 3.8 25.1 - - + -
129K GLU 3.4 4.3 - - - -
130K PRO* 3.8 24.2 - - + -
235K ILE* 4.2 13.9 - - + -
239K LYS* 6.4 0.2 - - - -
267K GLY* 1.3 74.1 - - - +
269K HIS* 1.3 67.7 + - - +
270K CYS* 3.4 5.0 + - - -
321K ARG* 4.4 0.2 - - - +
361K PRO* 2.7 35.0 + - + +
362K ASP 3.6 29.2 - - - +
363K PRO* 3.7 11.2 - - + +
365K ALA* 4.3 19.1 - - + +
367K PRO* 5.2 4.3 - - + -
370K CYS* 4.9 1.8 - - - -
371K PHE* 4.3 20.9 - - + -
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Residues in contact with HIS 269 (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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50J ASP* 5.5 4.9 - - - -
127K GLY 3.7 0.9 - - - +
128K PRO* 3.1 4.3 - - - +
129K GLU* 2.7 45.3 + - + +
131K GLU* 5.7 7.7 + - - -
267K GLY* 5.2 1.9 - - - -
268K MET* 1.3 77.2 - - - +
270K CYS* 1.3 59.7 + - - +
271K HIS 4.0 0.4 - - - -
321K ARG* 4.5 9.6 + - - -
329K PRO* 5.6 1.0 - - - +
357K GLU* 3.0 16.2 + - + +
358K VAL 3.5 6.3 - - - +
359K ARG* 3.4 62.1 + - + +
470K MN 2.3 32.9 + - - -
1481K ADP 4.8 2.4 + - - -
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Residues in contact with CYS 270 (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* 4.7 11.2 - - + -
127K GLY 4.0 2.9 - - - -
128K PRO* 4.4 7.4 - - + -
268K MET* 3.4 18.8 - - - -
269K HIS* 1.3 75.3 - - - +
271K HIS* 1.3 60.7 + - - +
272K MET* 3.7 8.3 + - + +
356K ILE 3.6 1.2 - - - +
357K GLU* 3.4 2.0 - - - -
358K VAL* 2.8 39.9 + - + +
361K PRO* 4.3 14.6 - - + -
370K CYS* 5.0 0.7 - - - -
371K PHE* 4.0 27.1 - - - -
374K LEU* 4.5 18.2 - - + -
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Residues in contact with HIS 271 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126K PHE* 3.5 1.7 - - - -
127K GLY 2.9 46.4 + - - +
129K GLU* 3.1 22.4 + - - -
269K HIS* 5.1 0.2 - - + -
270K CYS* 1.3 73.3 - - - +
272K MET* 1.3 64.5 + - - +
344K ARG* 4.8 3.4 - - - -
346K PRO* 4.1 10.3 - - + +
355K ARG* 2.9 29.2 + - - -
356K ILE 3.2 6.3 + - - +
357K GLU* 3.0 42.1 + - + +
1481K ADP 3.2 47.9 + - + -
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Residues in contact with MET 272 (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* 6.0 0.9 - - + -
125K LEU 3.2 7.4 - - - +
126K PHE* 3.5 42.4 - - + -
270K CYS* 3.9 10.8 - - + +
271K HIS* 1.3 80.5 - - - +
273K SER* 1.3 61.7 + - - +
282K PHE* 4.0 2.8 - - - -
297K TYR* 3.6 28.3 - - + +
301K VAL* 5.2 0.4 - - + -
355K ARG* 3.0 21.6 - - - +
356K ILE* 2.8 34.6 + - + +
358K VAL* 3.2 35.9 - - + -
374K LEU* 3.9 17.3 - - + -
1481K ADP 4.5 2.6 + - - -
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Residues in contact with SER 273 (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* 3.9 3.1 - - - +
125K LEU* 2.9 40.1 + - - +
272K MET* 1.3 79.2 - - - +
274K LEU* 1.3 65.8 + - - +
275K ALA* 5.7 0.2 - - - +
280K ASN* 3.9 12.3 + - - -
282K PHE* 3.8 13.4 - - - -
297K TYR* 6.1 0.2 - - - -
354K ARG 3.7 16.8 - - - -
355K ARG* 3.9 0.7 - - - -
1481K ADP 2.9 29.1 + - - -
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Residues in contact with LEU 274 (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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115K LEU* 3.9 16.8 - - + -
120K ILE* 4.8 4.3 - - + -
121K ALA* 4.0 13.7 - - + -
123K THR 3.7 9.2 - - - +
124K VAL* 3.3 33.0 - - + -
125K LEU* 5.8 0.4 - - - -
273K SER* 1.3 76.1 + - - +
275K ALA* 1.3 62.7 + - - +
280K ASN* 3.4 8.0 - - - +
281K LEU* 3.1 27.3 + - + +
282K PHE* 3.5 30.4 - - + -
293K GLN* 5.1 1.6 - - - +
297K TYR* 3.8 22.0 - - + -
375K LEU* 4.4 4.3 - - + -
379K LEU* 4.3 9.4 - - + -
382K ILE* 4.1 14.6 - - + -
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Residues in contact with ALA 275 (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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121K ALA* 3.2 4.7 - - - +
122K ASP* 2.8 29.9 + - - +
123K THR* 3.1 23.7 + - - +
125K LEU* 5.0 13.0 - - + -
274K LEU* 1.3 78.7 - - - +
276K LYS* 1.3 61.1 + - - +
278K GLY* 5.2 4.7 - - - +
279K THR 3.2 19.3 - - - +
280K ASN* 4.7 1.6 - - - -
281K LEU* 4.0 2.2 - - - -
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Residues in contact with LYS 276 (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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119K GLY* 2.9 35.9 + - - +
120K ILE 4.6 3.8 - - - +
121K ALA* 4.3 12.0 - - - +
122K ASP* 3.2 17.1 + - - +
275K ALA* 1.3 74.5 - - - +
277K ASN* 1.3 88.7 + - - +
278K GLY 3.2 0.9 - - - -
279K THR* 2.8 26.1 + - - -
281K LEU* 3.5 18.1 - - + +
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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