Contacts of the strand formed by residues 250 - 255 (chain B) in PDB entry 1AHF
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 LEU 250 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A PHE* 4.9 1.2 - - - -
88B PHE* 4.8 4.0 - - + -
218B LEU* 4.1 5.3 - - - +
219B PRO* 3.5 21.1 - - + +
221B PHE* 5.1 3.1 - - + -
240B LEU* 4.6 9.2 - - + -
243B PHE* 4.1 14.6 - - + -
244B ALA* 3.9 33.7 - - + +
247B HIS* 4.1 11.7 - - + -
249B GLU* 1.3 76.4 - - - +
251B ILE* 1.3 68.6 + - - +
252B VAL* 4.1 19.3 - - + -
272B LEU* 4.4 0.5 - - - +
273B VAL* 2.8 65.6 + - + +
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Residues in contact with ILE 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A PHE* 4.1 7.0 - - + -
115B ALA* 4.1 10.5 - - + -
118B PHE* 4.8 2.5 - - + -
119B LEU* 3.5 35.2 - - + -
218B LEU* 3.6 19.1 - - + -
219B PRO 2.9 8.9 + - - +
220B LEU* 3.1 26.7 - - + +
221B PHE* 2.7 31.7 + - - +
250B LEU* 1.3 79.4 - - - +
252B VAL* 1.3 65.8 + - - +
253B ALA* 5.6 0.2 - - - -
270B CYS* 4.0 21.8 - - - -
271B THR 3.3 7.6 - - - +
272B LEU* 3.6 19.7 - - + -
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Residues in contact with VAL 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B LEU* 4.7 11.9 - - + -
88B PHE* 4.4 13.0 - - + -
221B PHE* 3.5 18.2 - - + +
223B PHE* 4.4 14.6 - - + -
240B LEU* 4.2 19.7 - - + -
250B LEU* 4.1 19.1 - - + -
251B ILE* 1.3 82.7 - - - +
253B ALA* 1.3 70.1 + - - +
254B SER* 4.3 6.9 + - - +
269B ALA 3.3 2.1 - - - +
270B CYS* 3.3 5.0 - - - -
271B THR* 2.7 51.2 + - - +
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Residues in contact with ALA 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B GLY* 4.4 3.8 - - - +
111B ALA* 4.1 17.3 - - + +
112B LEU* 3.5 36.8 - - + -
115B ALA* 6.0 0.2 - - + -
220B LEU* 4.5 4.7 - - + +
221B PHE 2.6 12.5 + - - +
222B ASP* 3.5 6.7 - - - +
223B PHE 2.8 24.7 + - - -
251B ILE* 4.3 0.4 - - + -
252B VAL* 1.3 75.5 - - - +
254B SER* 1.3 59.5 + - - +
269B ALA 3.4 5.6 - - - -
270B CYS* 5.5 0.7 - - - -
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Residues in contact with SER 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B THR* 4.1 12.7 - - - +
87B LEU* 4.6 16.2 - - - +
108B GLY* 3.6 8.6 - - - -
223B PHE* 3.3 21.3 - - - -
226B GLN* 5.9 1.3 - - - -
252B VAL* 3.8 3.9 + - - +
253B ALA* 1.3 74.3 - - - +
255B SER* 1.3 65.3 + - - +
256B TYR* 5.2 5.8 - - - -
268B GLY* 3.2 3.2 - - - -
269B ALA* 2.8 45.8 + - - +
271B THR* 5.3 0.5 + - - -
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Residues in contact with SER 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B GLY* 3.8 7.2 - - - -
223B PHE 3.1 10.1 + - - +
224B ALA* 4.1 30.0 - - - +
226B GLN* 5.7 0.5 + - - +
254B SER* 1.3 80.5 - - - +
256B TYR* 1.3 69.1 + - - +
257B SER* 3.0 15.6 + - - -
258B LYS* 4.6 1.0 + - - +
259B ASN* 4.1 12.0 + - - +
267B VAL 3.8 3.9 + - - -
268B GLY* 4.0 0.4 - - - -
412B PLP 2.4 30.8 + - - -
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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