Contacts of the strand formed by residues 325 - 337 (chain A) in PDB entry 1L9N
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 325 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A SER 4.0 0.3 - - - +
299A ALA* 3.4 3.1 - - - +
300A HIS* 2.8 40.2 + - - +
308A VAL* 4.4 2.2 - - - +
309A ASP 5.4 2.7 - - - -
310A VAL* 6.0 2.0 - - - -
323A SER 5.0 1.1 - - - -
324A ASP* 1.3 80.1 - - - +
326A VAL* 1.3 65.0 + - - +
327A TRP* 3.1 26.7 + - - -
526A ASN 4.6 5.4 - - - -
527A GLY* 6.3 0.2 - - - -
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Residues in contact with VAL 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A ASN* 4.0 22.2 - - + +
298A SER 3.4 7.6 - - - +
299A ALA* 4.5 0.7 - - + -
308A VAL* 3.8 25.1 - - + -
310A VAL* 4.3 21.3 - - + +
325A SER* 1.3 79.6 - - - +
327A TRP* 1.3 72.8 + - - +
328A ASN 4.1 0.5 + - - -
396A ARG* 4.3 13.9 - - - +
418A ILE* 4.1 14.6 - - + -
526A ASN 3.3 10.7 - - - +
527A GLY* 4.5 4.2 - - - -
570A ARG* 5.1 6.2 + - - -
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Residues in contact with TRP 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A TRP* 3.8 28.3 - + - -
272A CYS* 4.3 2.7 - - + -
297A ASN* 3.2 6.6 - - - +
298A SER* 2.7 39.4 + - - +
300A HIS* 4.8 3.2 + - + +
325A SER* 3.1 25.4 + - - -
326A VAL* 1.3 75.5 - - - +
328A ASN* 1.3 67.2 + - - +
329A PHE 3.0 24.5 + - - +
330A HIS* 3.8 25.4 - - + -
355A THR* 4.4 0.9 - - + -
357A GLN* 3.2 36.5 + - + -
525A TYR* 3.5 28.0 - + - -
526A ASN* 3.3 37.3 + - + +
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Residues in contact with ASN 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A GLY 4.0 15.4 + - - +
166A SER* 4.6 6.6 - - - -
167A THR* 4.6 1.9 - - - +
296A PHE* 3.4 11.1 - - - +
297A ASN* 3.0 22.0 + - - +
326A VAL 4.1 1.0 + - - -
327A TRP* 1.3 70.6 - - - +
329A PHE* 1.3 67.0 + - + +
523A ILE* 4.0 7.7 - - - +
525A TYR* 2.8 42.2 + - - +
526A ASN 4.7 0.2 - - - -
527A GLY* 5.5 0.6 - - - -
568A MET* 3.3 30.1 - - + +
570A ARG* 4.6 2.8 + - - -
588A ASP* 2.8 25.5 - - - +
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Residues in contact with PHE 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A VAL* 3.7 27.1 - - + -
165A GLY* 3.1 36.6 - - - -
247A ARG* 4.6 7.2 - - - -
272A CYS* 4.2 0.7 - - - -
273A TRP* 4.1 17.3 - + - -
294A THR* 4.1 7.9 - - + -
295A ASN 3.0 11.7 - - - +
296A PHE* 3.5 20.9 - + + -
298A SER* 4.4 0.4 - - - -
327A TRP* 2.9 13.1 - - - +
328A ASN* 1.3 84.8 - - + +
330A HIS* 1.3 63.0 + - - +
331A VAL* 3.8 22.9 - - + -
525A TYR* 3.2 57.2 + + + -
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Residues in contact with HIS 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A CYS* 3.1 28.7 - - + +
293A ILE 3.9 0.7 - - - +
294A THR* 3.7 0.2 - - - -
295A ASN* 2.8 33.5 + - - +
298A SER* 3.4 20.0 - - - +
327A TRP* 3.8 13.0 - + + -
329A PHE* 1.3 76.2 - - - +
331A VAL* 1.3 76.9 + - - +
332A TRP* 3.4 17.6 - + - -
353A ASP* 2.6 23.5 + - - -
355A THR* 3.4 20.2 - - + -
357A GLN* 3.1 17.9 + - - -
391A GLU* 3.0 24.7 - - - -
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Residues in contact with VAL 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ILE* 3.9 11.2 - - + -
163A PHE 4.2 0.2 - - - +
272A CYS* 3.3 12.3 - - - +
273A TRP* 3.9 23.6 - - + +
276A ALA* 3.6 11.5 - - + +
292A VAL* 3.2 35.2 - - + -
293A ILE 3.1 7.2 - - - +
294A THR* 3.6 16.8 - - - +
329A PHE* 3.8 24.0 - - + -
330A HIS* 1.3 100.5 + - - +
332A TRP* 1.3 61.1 + - - +
353A ASP* 4.0 2.6 - - - +
355A THR* 4.2 0.3 + - - -
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Residues in contact with TRP 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A ALA* 4.2 2.5 - - - -
292A VAL* 3.5 7.8 - - - +
293A ILE* 2.7 55.4 + - + +
295A ASN* 3.6 29.2 - - + -
298A SER* 4.0 0.9 - - - -
330A HIS* 3.4 27.6 - + - -
331A VAL* 1.3 73.5 - - - +
333A ASN* 1.3 91.9 + - - +
351A VAL* 3.7 17.5 - - + +
352A LEU 3.7 2.9 - - - +
353A ASP* 3.7 23.6 - - + +
388A ILE* 5.0 4.3 - - + -
391A GLU* 3.6 28.0 - - + -
392A VAL* 3.5 26.0 - - + -
422A ILE* 5.1 0.4 - - + -
439A TYR* 2.8 44.0 + + - -
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Residues in contact with ASN 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A ALA* 2.8 43.2 + - - +
279A LEU* 3.4 23.4 - - + +
280A ASN* 3.2 31.1 - - - +
283A LEU* 4.5 9.0 - - + -
291A ARG 3.4 6.7 - - - +
292A VAL* 4.0 4.8 - - - +
293A ILE 4.5 0.4 - - - +
332A TRP* 1.3 85.9 - - - +
334A GLU* 1.3 65.8 + - - +
351A VAL* 3.3 5.5 - - - -
352A LEU* 2.8 38.2 + - + +
353A ASP* 5.1 0.9 - - - -
354A ALA 5.1 0.7 + - - -
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Residues in contact with GLU 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A LEU* 5.3 0.2 - - - -
290A SER* 3.1 25.9 - - - -
291A ARG* 2.8 45.9 + - + -
293A ILE* 3.3 23.5 - - + +
333A ASN* 1.3 78.8 - - - +
335A GLY* 1.3 58.7 + - - +
349A TRP* 3.4 29.2 - - + -
350A GLN 3.0 9.0 - - - +
351A VAL* 4.7 0.9 - - - -
352A LEU* 5.1 0.7 - - - -
371A VAL* 3.6 8.6 - - + +
435A VAL* 5.1 0.2 - - - +
439A TYR* 2.4 43.0 + - - +
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Residues in contact with GLY 335 (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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288A ILE* 4.2 6.3 - - - -
289A PRO 3.4 7.4 - - - -
290A SER* 4.3 2.9 - - - -
334A GLU* 1.3 75.0 - - - +
336A TRP* 1.3 59.6 + - - -
337A PHE* 4.0 16.8 - - - -
348A GLY 3.4 1.2 - - - +
349A TRP* 3.4 4.7 - - - -
350A GLN* 2.6 37.4 + - - +
352A LEU* 4.4 10.1 - - - +
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Residues in contact with TRP 336 (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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143A VAL* 3.6 20.0 - - - +
144A PHE 2.8 30.1 + - - -
145A MET* 3.6 26.5 - - + +
150A GLU* 6.0 2.2 - - - -
288A ILE* 4.1 0.4 - - - +
289A PRO* 2.8 34.0 + - + +
335A GLY* 1.3 72.1 - - - -
337A PHE* 1.3 73.6 + - - +
348A GLY* 3.4 25.4 - - - -
349A TRP* 3.4 54.5 - + + -
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Residues in contact with PHE 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A SER 3.2 16.8 - - - +
143A VAL* 4.1 0.7 - - - -
212A PRO* 3.6 45.5 - - + -
213A LYS* 3.8 23.8 - - + -
288A ILE* 4.0 14.1 - - + -
335A GLY* 4.0 15.7 - - - -
336A TRP* 1.3 93.3 - - - +
338A VAL* 1.3 76.7 + - - +
339A ARG* 3.9 5.4 - - - -
348A GLY 3.2 27.9 + - - +
350A GLN* 3.3 35.7 + - + -
352A LEU* 4.7 9.6 - - + -
368A PRO* 3.8 14.4 - - + -
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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