Contacts of the strand formed by residues 248 - 258 (chain A) in PDB entry 3HFV
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 GLU 248 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244A ASN* 3.2 9.7 + - - +
245A PHE 2.8 33.6 + - - +
246A HIS* 4.3 5.0 - - + +
247A GLY* 1.3 80.7 - - - +
249A TRP* 1.3 63.8 + - - +
250A LEU* 3.3 28.5 + - + +
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Residues in contact with TRP 249 (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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224A GLU* 3.6 25.6 - - + -
225A ILE 3.5 34.8 - - - -
226A ARG* 2.9 60.2 - - + +
242A GLU* 3.4 16.7 - - + +
243A ILE 3.6 5.6 - - - -
244A ASN* 2.9 42.7 - - + +
248A GLU* 1.3 74.3 - - - +
250A LEU* 1.3 63.9 + - - +
251A GLU* 4.0 2.9 + - - +
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Residues in contact with LEU 250 (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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150A GLN* 5.0 11.4 - - - +
242A GLU* 3.1 2.4 - - - -
243A ILE* 2.6 42.2 + - - +
245A PHE* 3.9 40.8 - - + +
248A GLU* 3.3 28.5 + - + +
249A TRP* 1.3 77.4 - - - +
251A GLU* 1.4 60.5 + - - +
252A VAL* 3.6 3.1 + - - +
282A ARG* 3.8 31.6 - - - +
286A ILE* 4.3 14.8 - - + -
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Residues in contact with GLU 251 (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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240A GLU* 4.5 26.6 - - + +
241A MET 3.4 7.9 - - - +
242A GLU* 3.7 22.1 - - + +
249A TRP 4.0 3.2 + - - +
250A LEU* 1.4 73.0 - - - +
252A VAL* 1.3 59.0 + - - +
253A LEU 4.7 3.4 - - - +
282A ARG* 2.6 51.4 + - - +
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Residues in contact with VAL 252 (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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215A MET* 4.4 7.6 - - + -
241A MET* 2.9 27.3 + - + +
243A ILE* 4.1 17.7 - - + -
250A LEU 3.8 7.6 - - - +
251A GLU* 1.3 79.0 - - - +
253A LEU* 1.3 66.5 + - + +
278A LEU* 3.5 4.0 - - + +
279A GLY* 3.2 23.3 + - - +
282A ARG* 3.7 22.2 - - + -
283A LEU* 3.9 25.7 - - + +
286A ILE* 3.7 24.2 - - + -
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Residues in contact with LEU 253 (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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211A LEU* 3.8 32.1 - - + -
215A MET* 4.0 21.8 - - + -
240A GLU* 3.3 24.8 - - - +
241A MET* 3.3 30.1 + - + +
251A GLU* 3.8 2.6 - - - +
252A VAL* 1.3 80.7 - - + +
254A GLY* 1.3 75.3 + - - +
255A CYS* 3.8 19.5 - - + -
276A PHE* 4.6 1.8 - - + -
277A GLY 3.1 16.4 - - - +
278A LEU* 3.6 11.7 - - + +
279A GLY 4.9 0.2 - - - +
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Residues in contact with GLY 254 (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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232A PHE* 3.9 12.8 - - - -
239A PHE 3.6 7.0 - - - -
240A GLU* 4.5 0.7 - - - -
253A LEU* 1.3 74.8 - - - +
255A CYS* 1.3 64.5 + - - +
276A PHE* 3.1 2.1 - - - +
277A GLY 2.8 30.8 + - - -
416A MTY 3.5 23.9 - - - +
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Residues in contact with CYS 255 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207A LEU* 3.5 20.6 - - + -
211A LEU* 4.1 8.3 - - - -
227A TRP* 4.3 6.3 - - - -
232A PHE* 4.1 1.3 - - - -
235A THR* 4.1 0.6 + - - -
238A SER* 3.2 9.8 - - - -
239A PHE* 2.9 49.9 + - - -
253A LEU* 3.8 14.6 - - + -
254A GLY* 1.3 76.0 - - - +
256A GLY* 1.3 58.5 + - - +
275A ALA 3.1 15.9 - - - +
276A PHE* 3.2 13.2 - - + -
416A MTY 3.5 13.5 - - - -
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Residues in contact with GLY 256 (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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207A LEU* 3.5 14.4 - - - +
235A THR* 3.8 9.0 - - - +
237A PRO 3.2 13.0 - - - -
238A SER* 4.0 1.3 - - - -
239A PHE* 4.4 4.3 - - - -
255A CYS* 1.3 79.9 - - - +
257A VAL* 1.3 65.3 + - - -
274A TRP* 3.3 5.6 - - - +
275A ALA 3.0 26.9 + - - -
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Residues in contact with VAL 257 (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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195A HIS* 3.6 33.2 - - + +
200A VAL* 4.3 13.9 - - + -
203A VAL* 3.9 20.9 - - + -
204A GLU* 4.7 10.8 - - + +
207A LEU* 5.9 0.7 - - + -
235A THR* 3.0 3.3 - - - -
236A HIS 2.6 41.7 + - - +
237A PRO* 3.0 23.8 + - + +
239A PHE* 5.7 1.8 - - + -
256A GLY* 1.3 72.1 - - - -
258A MET* 1.3 64.0 + - - +
272A ILE* 4.3 10.1 - - + -
273A GLY 3.5 13.0 - - - +
274A TRP* 4.4 0.7 - - + +
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Residues in contact with MET 258 (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 GLN* 3.4 28.7 - - - +
128A LEU* 3.9 25.6 - - + -
161A VAL* 3.7 21.3 - - + -
163A LEU* 4.2 8.1 - - - -
192A GLN* 3.0 12.1 + - - +
195A HIS* 4.0 3.5 - - - -
234A PHE 3.8 7.9 - - - +
235A THR* 3.9 2.0 - - + -
257A VAL* 1.3 74.8 - - - +
259A GLU* 1.3 67.2 + - - +
260A GLN* 3.1 5.4 + - - +
262A LEU* 4.1 7.6 - - + -
263A VAL* 3.8 17.4 - - + +
273A GLY* 3.0 22.5 + - - +
274A TRP 3.5 27.8 - - - +
275A ALA* 3.9 8.7 - - + -
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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