Contacts of the strand formed by residues 255 - 263 (chain A) in PDB entry 3LEZ
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 THR 255 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A PHE* 5.4 1.3 - - + -
82A ALA* 3.6 28.7 + - + +
84A THR* 4.1 10.1 - - + +
185A ALA* 3.5 13.2 - - - +
250A ALA* 3.2 6.9 - - - +
251A GLY* 3.1 31.3 + - - +
252A GLY 2.8 20.5 + - - -
253A TYR* 4.7 0.2 - - - +
254A GLY* 1.3 76.9 - - - +
256A ARG* 1.3 63.8 + - - +
257A ASN* 3.6 13.7 - - - +
277A SER 3.1 13.2 - - - +
278A SER* 3.7 15.0 - - - +
286A TYR* 4.0 3.6 - - - -
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Residues in contact with ARG 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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229A THR 4.8 6.3 + - - -
233A LEU* 3.7 24.1 - - + +
248A THR* 4.0 6.9 - - - -
249A GLY 3.1 15.2 + - - -
250A ALA* 3.8 4.9 - - - +
254A GLY 3.4 0.8 + - - +
255A THR* 1.3 74.5 - - - +
257A ASN* 1.3 66.0 + - - +
276A MET 3.8 0.2 - - - -
277A SER* 2.8 39.6 + - - +
286A TYR* 3.2 51.9 + - + -
287A ASP 5.3 1.6 - - - +
288A ASP* 3.0 31.6 + - - +
290A LEU* 5.9 0.9 - - + -
291A ILE* 3.8 25.3 - - + +
305A EPE 2.9 31.1 + - - +
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Residues in contact with ASN 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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81A PHE* 4.9 0.3 - - - +
82A ALA 2.9 27.1 + - - +
83A TYR 3.2 18.0 + - - -
84A THR* 3.6 7.1 + - - -
86A THR* 3.7 16.4 - - + +
233A LEU* 3.9 6.6 - - - +
248A THR* 3.4 3.5 - - - -
249A GLY 2.9 30.5 + - - +
255A THR* 3.6 10.1 - - - +
256A ARG* 1.3 82.3 - - - +
258A ASP* 1.3 64.1 + - - +
259A ILE* 5.5 0.4 - - + -
275A ILE 3.2 9.0 - - - +
276A MET* 3.2 29.8 - - + +
277A SER 3.2 5.0 + - - -
291A ILE* 5.1 1.8 - - - -
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Residues in contact with ASP 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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230A GLY 4.7 0.5 - - - +
233A LEU* 3.2 12.1 - - + +
234A ILE* 3.0 49.1 + - + +
246A ASP* 2.5 30.2 - - - +
247A LYS 3.0 17.0 - - - +
248A THR* 3.5 4.2 + - - -
257A ASN* 1.3 75.5 - - - +
259A ILE* 1.3 64.1 + - - +
275A ILE* 2.9 31.5 + - - +
291A ILE* 3.9 17.2 - - + +
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Residues in contact with ILE 259 (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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86A THR* 3.7 38.1 - - + +
89A PRO* 4.3 10.3 - - + -
90A LEU* 4.9 2.5 - - + -
199A MET* 3.9 26.0 - - + +
200A ALA* 5.7 0.4 - - - +
203A LEU* 4.1 27.3 - - + +
224A LEU* 5.4 0.6 - - + +
234A ILE* 4.1 4.0 - - - -
246A ASP* 3.1 3.6 - - - +
247A LYS* 2.8 45.2 + - + +
257A ASN* 5.5 0.2 - - + -
258A ASP* 1.3 79.7 - - - +
260A GLY* 1.3 59.7 + - - +
273A ILE 3.4 8.1 - - - +
274A ALA* 3.7 20.9 - - + -
275A ILE 4.6 2.7 - - - +
276A MET* 5.4 3.8 - - + -
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Residues in contact with GLY 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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203A LEU* 3.7 12.2 - - - +
224A LEU* 6.0 0.7 - - - -
234A ILE* 4.2 3.2 - - - +
244A VAL* 5.7 0.4 - - - -
245A GLY 3.0 13.0 - - - -
246A ASP* 4.0 2.7 - - - -
259A ILE* 1.3 76.5 - - - +
261A ILE* 1.3 70.8 + - - +
273A ILE* 2.8 41.1 + - - +
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Residues in contact with ILE 261 (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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203A LEU* 4.1 17.7 - - + -
204A GLN* 4.8 2.9 - - - -
207A VAL* 4.0 20.4 - - + -
208A LEU* 4.3 13.7 - - + -
224A LEU* 5.4 4.0 - - + -
244A VAL* 3.4 4.5 - - - +
245A GLY* 2.9 31.2 + - - +
260A GLY* 1.3 84.3 - - - +
262A ILE* 1.3 64.2 + - - +
263A TRP* 3.5 36.5 - - + -
270A PRO* 3.8 20.6 - - + -
271A ILE 3.4 4.5 - - - +
272A VAL* 3.8 30.1 - - + -
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Residues in contact with ILE 262 (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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234A ILE* 4.0 14.8 - - + -
238A VAL* 3.9 24.9 - - + -
242A TRP* 3.6 35.0 - - + -
243A THR 3.5 7.2 - - - +
244A VAL* 4.3 4.9 - - + -
261A ILE* 1.3 77.2 - - - +
263A TRP* 1.3 63.9 + - - +
264A PRO* 3.4 4.8 - - + +
270A PRO* 3.2 4.0 - - - +
271A ILE* 2.8 51.0 + - + +
273A ILE* 3.9 32.3 - - + -
295A THR* 4.7 1.8 - - + -
299A LEU* 4.4 15.9 - - + -
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Residues in contact with TRP 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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207A VAL* 4.4 6.3 - - + -
208A LEU* 4.3 13.6 - - + +
221A THR* 3.7 28.9 - - + -
224A LEU* 6.4 1.1 - - + -
225A ILE* 4.1 13.9 - - + -
242A TRP* 3.7 0.9 - - - -
243A THR* 2.8 57.2 + - + +
245A GLY* 4.0 11.9 - - - -
261A ILE* 3.5 43.3 - - + -
262A ILE* 1.3 73.4 - - - +
264A PRO* 1.3 72.0 - - - +
265A GLU* 3.5 0.7 + - - -
268A GLU 4.4 7.9 - - - +
270A PRO* 3.7 28.0 - - + +
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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