Contacts of the strand formed by residues 251 - 258 (chain E) in PDB entry 2HU4
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 SER 251 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218E TRP* 2.6 34.4 + - - -
219E ARG* 3.9 14.8 - - - +
242E THR* 3.3 5.5 - - - +
243E ASP 2.9 40.1 + - - -
250E ALA* 1.3 70.8 - - - +
252E TYR* 1.3 63.6 + - - +
267E GLU* 2.9 26.7 + - - -
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Residues in contact with TYR 252 (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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240E VAL* 5.3 3.6 - - + -
241E MET 3.4 5.8 - - - +
242E THR* 3.5 15.3 - - + +
249E GLN* 4.0 4.7 + - - -
250E ALA* 3.0 49.4 + - + -
251E SER* 1.3 78.5 + - - +
253E LYS* 1.3 62.3 + - - +
267E GLU* 3.1 10.6 - - - +
268E LEU* 2.9 50.8 + - + -
270E ALA* 4.4 17.7 - - + -
273E TYR 2.8 31.4 + - - -
274E HIS* 3.3 14.7 - + - -
275E TYR* 3.5 40.8 - + + -
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Residues in contact with LYS 253 (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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218E TRP* 3.6 58.1 - - + +
239E THR 3.9 0.2 - - - +
240E VAL* 3.3 8.8 - - - +
241E MET 2.9 34.3 + - - -
252E TYR* 1.3 80.1 - - - +
254E ILE* 1.3 65.6 + - - +
255E PHE* 3.7 26.4 - - + -
265E SER* 5.1 8.3 + - - +
266E VAL 3.2 15.3 - - - +
267E GLU* 3.8 24.2 - - + +
268E LEU* 4.7 0.4 - - - +
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Residues in contact with ILE 254 (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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239E THR 3.5 7.6 - - - +
240E VAL* 4.7 7.2 - - + -
253E LYS* 1.3 76.5 - - - +
255E PHE* 1.3 67.0 + - - +
265E SER* 3.1 5.2 - - - -
266E VAL* 2.9 31.6 + - + +
268E LEU* 3.4 34.8 - - + -
303E VAL* 4.0 5.6 - - + -
305E PHE* 3.2 65.1 - - + -
310E LEU* 3.8 21.6 - - + +
312E TYR* 4.3 8.1 - - + -
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Residues in contact with PHE 255 (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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215E ILE* 3.7 43.7 - - + -
218E TRP* 4.1 13.5 - + - -
237E CYS 3.7 0.7 - - - +
238E PHE* 3.4 9.9 - - - +
239E THR* 3.0 43.0 + - + +
241E MET* 3.7 35.4 - - + -
253E LYS* 3.7 29.2 - - + -
254E ILE* 1.3 79.0 - - - +
256E LYS* 1.3 60.4 + - - +
257E MET* 4.1 11.6 - - - +
262E VAL* 4.0 12.6 - - + -
264E LYS 3.6 2.2 - - - +
265E SER* 3.8 19.3 - - - -
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Residues in contact with LYS 256 (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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236E SER* 3.4 27.6 - - - -
237E CYS 3.7 3.4 - - - -
238E PHE* 3.5 21.1 - - + -
255E PHE* 1.3 72.5 - - - +
257E MET* 1.3 66.5 + - - +
258E GLU* 3.7 11.3 + - - -
262E VAL* 3.4 3.3 - - - +
263E VAL* 2.8 38.7 + - + +
264E LYS* 2.7 28.1 + - + +
308E GLN* 3.1 31.0 + - - +
309E ASN* 4.4 8.9 + - - -
310E LEU* 3.9 11.4 - - + +
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Residues in contact with MET 257 (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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190E LEU* 3.9 20.4 - - + +
192E ILE* 3.5 18.6 - - + -
205E LEU* 3.8 24.2 - - - -
215E ILE* 5.4 1.1 - - - -
230E CYS* 5.0 1.1 - - + -
235E GLY 4.6 0.2 - - - +
237E CYS* 3.0 43.0 + - - +
238E PHE 4.3 1.8 - - - -
239E THR* 3.3 46.0 - - + +
255E PHE* 4.4 8.7 - - - +
256E LYS* 1.3 79.2 - - - +
258E GLU* 1.3 63.2 + - - +
259E LYS 4.3 0.6 + - - -
260E GLY* 4.6 3.3 + - - -
261E LYS 3.0 27.6 - - - +
262E VAL* 3.7 4.5 - - - +
263E VAL* 4.1 1.3 - - - +
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Residues in contact with GLU 258 (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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235E GLY 3.7 16.4 - - - +
236E SER* 2.8 28.7 + - - +
256E LYS* 3.7 12.6 + - - -
257E MET* 1.3 75.4 - - - +
259E LYS* 1.3 76.8 + - + +
260E GLY 3.2 1.1 - - - -
261E LYS* 2.8 24.3 + - - +
263E VAL* 3.7 27.9 - - + +
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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