Contacts of the strand formed by residues 251 - 258 (chain A) in PDB entry 1L7R
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 ALA 251 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A TRP* 3.9 22.0 - - + -
137A ILE* 3.2 22.0 - - + -
139A PRO* 4.5 0.7 - - + -
249A THR 3.4 5.7 + - - +
250A PRO* 1.3 74.6 - - - +
252A LEU* 1.3 59.2 + - - +
253A ILE* 3.5 13.2 + - + +
272A VAL* 4.4 7.2 - - + -
277A ASP 3.2 7.1 + - - -
278A ALA* 3.3 4.4 - - - +
279A ARG 2.9 26.7 + - - +
317A PHE* 3.6 3.8 - - - -
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Residues in contact with LEU 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ILE 2.9 8.9 + - - -
138A ALA* 3.1 30.3 - - + +
139A PRO* 3.7 0.9 - - - +
251A ALA* 1.3 69.4 - - - +
253A ILE* 1.3 65.2 + - - +
254A THR* 4.0 17.3 + - - +
279A ARG* 3.9 9.6 - - + -
281A VAL* 4.5 4.7 - - + -
313A MET* 3.9 33.2 - - + +
314A HIS* 3.6 52.9 + - + +
317A PHE* 3.5 31.1 - - + -
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Residues in contact with ILE 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A TRP* 4.0 14.6 - - + -
139A PRO* 3.5 13.0 - - + +
251A ALA* 4.1 20.4 - - + +
252A LEU* 1.3 76.5 - - - +
254A THR* 1.3 71.3 + - - +
265A SER* 3.7 25.8 - - - +
268A THR* 3.4 23.3 - - - +
269A PHE* 3.4 30.1 - - + +
272A VAL* 4.3 3.8 - - + -
279A ARG 2.9 12.6 + - - +
280A LEU* 3.3 18.4 - - + +
281A VAL* 2.9 24.6 + - - +
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Residues in contact with THR 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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139A PRO 3.3 7.3 + - - +
140A SER* 3.4 26.2 - - - +
141A MET* 2.8 29.6 + - + -
252A LEU* 4.0 15.3 + - - +
253A ILE* 1.3 79.3 + - - +
255A ALA* 1.3 63.4 + - - +
265A SER* 4.1 1.7 + - - -
281A VAL* 3.2 20.6 - - + +
285A TRP* 4.1 22.9 - - + -
305A TYR* 4.5 14.7 + - + +
314A HIS* 4.7 8.7 - - - -
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Residues in contact with ALA 255 (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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141A MET* 4.3 12.1 - - - +
254A THR* 1.3 76.7 - - - +
256A GLY* 1.3 59.5 + - - +
259A ASP* 5.7 0.4 - - - +
262A VAL* 4.4 12.3 - - + -
265A SER* 3.7 24.9 - - - +
266A LEU* 4.8 5.8 - - + -
280A LEU* 5.0 2.0 - - + -
281A VAL 2.8 6.9 + - - +
282A VAL* 3.3 21.8 - - + -
283A GLY 3.1 20.4 + - - -
285A TRP* 3.6 9.4 - - - -
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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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141A MET* 4.1 6.4 - - - +
255A ALA* 1.3 77.6 - - - +
257A TRP* 1.3 66.4 + - - -
258A TYR 3.1 3.6 - - - -
259A ASP* 3.0 23.0 + - - +
262A VAL* 3.1 17.6 - - - +
282A VAL* 4.2 1.1 - - - -
283A GLY 3.1 10.5 - - - -
285A TRP* 3.6 13.2 - - - -
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Residues in contact with TRP 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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256A GLY* 1.3 71.2 - - - -
258A TYR* 1.3 70.5 + - + +
259A ASP 3.4 0.8 + - - -
262A VAL* 4.2 12.3 - - + +
266A LEU* 4.3 7.0 - - + -
282A VAL* 3.4 36.2 + - + +
283A GLY 2.8 24.0 + - - +
284A PRO* 3.7 9.9 - - + -
285A TRP 3.8 0.8 + - - +
337A LEU* 4.1 11.2 - - + -
338A PHE 2.9 24.3 + - - -
340A MET* 3.7 29.4 - - + -
351A TRP* 3.8 31.9 - + - -
405A THR* 4.0 10.2 - - - +
476A LEU 4.4 7.5 - - - +
477A CYS* 5.8 0.5 - - - +
509A ALA* 3.9 17.1 - - + +
510A THR* 3.6 27.1 - - - +
511A SER* 3.3 28.1 - - - -
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Residues in contact with TYR 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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257A TRP* 1.3 80.5 - - + +
259A ASP* 1.3 60.3 + - - +
260A GLY 3.9 0.5 + - - -
284A PRO 3.7 16.6 - - - -
285A TRP 3.0 14.3 + - - +
286A SER* 3.3 17.5 - - - -
287A HIS 4.2 0.7 + - - -
299A PHE* 4.1 3.8 - + - -
340A MET* 3.8 27.9 - - + -
404A GLY* 3.4 27.4 - - - +
405A THR* 3.4 12.0 - - + -
406A LEU 4.5 0.5 - - - +
414A GLY* 3.3 31.4 - - - -
415A PRO* 3.6 26.9 - - + +
474A ILE* 4.5 1.0 - - - +
475A ALA 2.6 28.0 + - - -
476A LEU* 3.3 39.8 - - - +
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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