Contacts of the strand formed by residues 258 - 266 (chain A) in PDB entry 5LG1
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 258 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A PRO 3.9 2.3 - - - +
245A PRO* 3.2 26.6 - - - +
249A ASP* 5.4 1.2 + - - -
256A THR* 3.7 19.6 + - + +
257A PRO* 1.3 79.6 - - - +
259A VAL* 1.3 63.5 + - - +
260A THR* 4.1 7.0 + - - +
305A VAL* 3.5 32.4 - - + +
306A LEU 3.4 5.2 - - - +
307A THR* 4.6 7.8 + - - +
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Residues in contact with VAL 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A LEU* 3.7 22.2 - - + -
243A PHE 3.6 11.9 - - - +
245A PRO* 3.8 21.8 - - + -
258A GLU* 1.3 72.1 - - - +
260A THR* 1.3 62.9 + - - +
277A TRP* 3.7 19.5 - - + -
305A VAL* 3.6 2.1 - - - -
306A LEU* 2.9 36.2 + - + +
308A VAL* 3.7 23.3 - - + +
313A TRP* 4.3 13.2 - - + -
319A TYR* 4.5 8.1 - - + -
336A ILE* 4.1 12.8 - - + -
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Residues in contact with THR 260 (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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241A PHE 3.8 1.0 - - - +
242A LEU* 3.2 6.5 - - - +
243A PHE* 2.8 45.2 + - - +
244A PRO 5.7 0.5 + - - -
258A GLU* 4.3 8.3 + - - +
259A VAL* 1.3 74.6 + - - +
261A CYS* 1.3 61.3 + - - +
262A VAL* 3.9 7.6 - - + -
303A VAL* 3.7 28.0 - - + -
304A SER 3.6 3.4 - - - +
305A VAL* 4.2 13.4 - - + +
7C NAG 3.6 35.3 + - - -
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Residues in contact with CYS 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A VAL* 3.6 24.5 - - - -
241A PHE 3.5 4.7 - - - -
242A LEU* 3.8 4.0 - - + -
260A THR* 1.3 72.0 - - - +
262A VAL* 1.3 61.2 + - - +
275A PHE* 4.1 12.5 - - + -
277A TRP* 3.5 18.5 - - + -
302A VAL 3.9 0.7 - - - +
303A VAL* 3.4 3.1 - - - +
304A SER* 2.8 38.3 + - - +
321A CYS* 2.0 49.6 - - - -
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Residues in contact with VAL 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A SER 3.8 0.7 - - - +
240A VAL* 3.4 4.0 - - - +
241A PHE* 2.9 41.4 + - + +
243A PHE* 4.0 23.6 - - + -
260A THR* 3.9 19.1 - - + -
261A CYS* 1.3 79.8 - - - +
263A VAL* 1.3 64.3 + - - +
264A VAL* 4.1 13.9 + - + -
301A ARG* 3.7 39.0 - - + +
302A VAL 3.5 7.0 - - - +
303A VAL* 4.0 10.5 - - + -
2C NAG 4.3 2.2 - - - +
7C NAG 4.5 3.1 - - - +
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Residues in contact with VAL 263 (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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238A PRO* 4.0 10.8 - - + -
239A SER 3.3 11.2 - - - +
240A VAL* 4.3 4.7 - - + -
262A VAL* 1.3 76.4 - - - +
264A VAL* 1.3 66.7 + - - +
266A VAL* 3.7 22.1 - - + +
273A VAL* 4.7 3.8 - - + -
275A PHE* 3.6 34.8 - - + -
300A TYR 4.0 0.3 - - - +
301A ARG* 3.3 8.0 - - - +
302A VAL* 2.8 43.4 + - + +
323A VAL* 3.8 28.7 - - + -
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Residues in contact with VAL 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A PRO* 3.4 5.2 - - - +
239A SER* 3.0 47.2 + - - +
241A PHE* 3.9 14.8 - - + -
262A VAL* 4.1 11.0 - - + -
263A VAL* 1.3 78.0 - - - +
265A ASP* 1.3 79.8 + - - +
266A VAL 3.2 3.4 + - - -
300A TYR 3.8 5.2 - - - +
301A ARG* 4.2 7.6 - - + +
1C NAG 3.5 16.8 - - - +
2C NAG 3.5 38.1 - - - +
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Residues in contact with ASP 265 (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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237A GLY 4.1 16.4 + - - +
238A PRO* 3.8 14.3 - - + +
239A SER* 4.0 13.2 + - - -
264A VAL* 1.3 84.1 - - - +
266A VAL* 1.3 62.5 + - - +
267A SER* 3.6 5.5 + - - -
270A ASP* 4.6 0.7 - - - +
299A THR* 3.8 19.9 + - + +
300A TYR 3.4 4.9 + - - -
1C NAG 2.5 51.1 + - - +
2C NAG 4.8 2.8 + - - -
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Residues in contact with VAL 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A PRO* 4.4 7.9 - - + -
263A VAL* 3.7 32.3 - - + +
264A VAL 3.2 0.9 - - - +
265A ASP* 1.3 77.8 - - - +
267A SER* 1.3 64.8 + - - +
270A ASP* 3.9 10.3 - - + +
273A VAL* 4.2 19.5 - - + -
292A ARG* 3.4 33.7 - - - +
299A THR* 3.6 4.1 - - - -
300A TYR* 2.7 49.8 + - + +
302A VAL* 4.5 8.3 - - + -
325A ASN* 5.7 0.7 - - - +
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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