Contacts of the strand formed by residues 257 - 262 (chain E) in PDB entry 1LWU
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 TYR 257 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247E TYR* 3.9 6.5 - - - -
248E ILE* 2.8 57.4 + - + +
250E PRO* 3.3 33.7 - - + +
254E SER* 6.2 2.5 - - - -
255E GLU 3.9 13.9 - - - +
256E PRO* 1.3 74.8 - - - +
258E LYS* 1.3 75.6 + - - +
259E VAL* 4.5 0.7 - - + -
293E GLU* 5.7 3.8 - - - +
314E LEU* 3.8 26.6 - - + +
318E THR* 2.9 34.4 - - + +
322E LEU* 4.7 6.4 - - - +
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Residues in contact with LYS 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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220E VAL* 5.3 2.9 - - - -
222E CYS* 3.9 23.9 + - - -
223E ARG 4.4 8.7 + - - -
224E VAL* 5.8 0.4 - - - +
225E PRO* 6.0 1.2 - - - +
245E ALA* 3.8 24.6 + - + +
246E TYR 3.2 12.6 - - - +
247E TYR* 4.0 28.6 - - + +
257E TYR* 1.3 81.3 - - - +
259E VAL* 1.3 62.5 + - - +
293E GLU* 4.8 2.9 - - - +
297E ILE* 3.6 34.2 - - + +
298E ALA 5.2 3.6 - - - +
306E CYS* 4.7 3.8 - - - -
314E LEU* 4.1 5.4 - - - +
140F ASP* 3.2 32.1 + - - +
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Residues in contact with VAL 259 (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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232E CYS* 4.0 21.3 - - - -
245E ALA* 3.6 0.9 - - - -
246E TYR 2.9 31.2 + - - +
248E ILE* 3.8 35.2 - - + -
257E TYR* 4.4 0.7 - - + +
258E LYS* 1.3 75.3 - - - +
260E PHE* 1.3 63.6 + - - +
261E CYS* 3.6 2.4 + - - -
271E THR* 3.6 15.3 - - + -
272E VAL 3.5 21.8 - - - +
297E ILE* 3.7 10.8 - - - -
312E TYR* 3.8 0.9 - - - +
314E LEU* 3.8 22.2 - - + -
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Residues in contact with PHE 260 (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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243E SER* 3.9 11.7 - - - -
244E GLU* 3.8 28.7 - - - -
259E VAL* 1.3 73.6 - - - +
261E CYS* 1.3 79.7 + - - +
262E ASP* 4.5 3.8 - - + -
271E THR* 4.1 0.3 - - - -
272E VAL* 3.0 42.4 + - + +
275E ASN* 6.2 0.4 - - - -
297E ILE* 3.6 26.1 - - + +
298E ALA* 3.9 8.5 - - + -
307E ASN 3.9 9.6 - - - -
308E ILE 4.1 0.7 - - - -
309E PRO* 3.4 45.1 - - + -
312E TYR* 3.1 25.8 + - + +
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Residues in contact with CYS 261 (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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232E CYS* 2.0 51.1 - - - -
235E ILE* 4.0 6.7 - - - -
243E SER* 3.3 14.6 - - - -
244E GLU 3.2 7.6 + - - -
246E TYR* 3.7 40.2 - - + -
259E VAL* 4.1 4.9 - - - -
260E PHE* 1.3 90.4 - - - +
262E ASP* 1.3 60.2 + - - +
263E MET* 3.4 14.1 - - + -
270E TRP 3.4 0.2 - - - -
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Residues in contact with ASP 262 (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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243E SER* 3.5 7.6 + - - -
260E PHE* 4.0 4.2 + - + -
261E CYS* 1.3 70.7 - - - +
263E MET* 1.3 58.8 + - - +
264E GLU* 3.1 4.8 + - - +
265E SER* 2.9 37.9 + - - -
268E GLY* 3.2 4.0 - - - -
269E GLY 3.2 2.1 + - - -
270E TRP* 2.8 45.0 + - + +
272E VAL* 4.3 5.2 - - + -
473E LYS* 2.6 39.7 + - - -
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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