Contacts of the strand formed by residues 349 - 362 (chain A) in PDB entry 2ARR
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 LEU 349 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A PHE* 4.4 12.6 - - + -
195A ARG* 3.6 34.5 - - + -
196A MET* 5.5 0.4 - - + -
338A ALA* 3.8 7.8 - - - +
340A PHE* 3.8 23.1 + - + +
343A MET* 3.8 37.7 - - + -
344A SER* 4.3 13.0 - - - -
347A ASN* 3.6 2.6 + - - +
348A ASP* 1.3 94.3 - - - +
350A PHE* 1.3 65.3 + - - +
355P MET* 4.3 14.8 - - + -
356P THR 3.3 14.6 - - - +
357P GLY* 4.2 0.2 - - - -
358P ARG* 3.7 15.4 + - - +
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Residues in contact with PHE 350 (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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321A ARG* 6.1 2.0 - - - -
332A ALA 4.0 1.8 - - - +
333A PHE 4.3 5.8 - - - -
334A ASN 4.2 0.2 - - - +
335A LYS* 3.8 57.7 - - + -
338A ALA* 3.5 22.0 - - + -
340A PHE* 4.1 2.7 - - - -
349A LEU* 1.3 74.8 - - - +
351A LEU* 1.3 71.5 + - - +
352A SER* 3.5 19.5 + - - -
355P MET* 3.4 9.2 - - - -
356P THR* 2.8 59.3 + - + -
357P GLY 3.9 14.6 - - - -
358P ARG* 4.1 9.6 - - + +
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Residues in contact with LEU 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A MET* 4.2 14.6 - - + -
42A VAL* 4.4 13.9 - - + -
332A ALA* 3.0 26.6 + - + +
333A PHE* 3.3 57.6 - - + +
340A PHE* 4.1 5.3 - - + -
350A PHE* 1.3 75.6 - - - +
352A SER* 1.3 61.3 + - - +
353A GLU 4.0 5.6 - - - +
354A VAL* 3.9 12.8 - - + -
353P GLY* 4.2 4.3 - - - -
354P VAL 3.5 27.8 - - - +
355P MET* 3.6 22.5 - - - +
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Residues in contact with SER 352 (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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189A SER 4.9 1.6 + - - -
321A ARG* 3.3 33.5 + - - +
333A PHE* 4.3 1.1 - - - -
350A PHE* 3.5 16.0 + - - -
351A LEU* 1.3 73.7 - - - +
353A GLU* 1.3 62.3 + - - +
354P VAL* 2.8 35.8 + - - +
356P THR* 3.0 25.5 + - - -
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Residues in contact with GLU 353 (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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319A GLU* 3.7 22.8 - - + +
320A LEU 3.2 4.5 + - - -
321A ARG* 2.8 50.6 + - - +
322A SER 5.2 0.2 + - - -
333A PHE* 4.3 5.3 - - - -
351A LEU* 3.6 2.2 - - - +
352A SER* 1.3 84.6 + - - +
354A VAL* 1.3 83.1 + - - +
355A PHE* 3.3 39.5 - - + -
352P GLY 4.0 0.5 - - - +
353P GLY* 3.8 0.2 - - - -
354P VAL* 3.1 26.9 + - - +
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Residues in contact with VAL 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A MET* 4.2 12.8 - - - -
318A TYR 3.9 0.2 - - - +
319A GLU* 3.4 2.9 - - - -
320A LEU* 2.8 48.8 + - + +
321A ARG 4.8 0.4 - - - +
324A LEU* 4.4 3.8 - - + -
333A PHE* 4.1 9.6 - - + -
351A LEU* 3.9 29.8 - - + -
353A GLU* 1.3 89.8 + - - +
355A PHE* 1.3 61.0 + - - +
351P MET* 3.0 37.7 - - + -
352P GLY 3.4 5.8 - - - +
353P GLY* 4.4 4.7 - - - -
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Residues in contact with PHE 355 (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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184A LEU* 3.7 18.8 - - + +
185A LEU* 3.8 20.6 - - + -
186A PRO* 3.4 30.5 - - + -
189A SER* 3.4 29.4 - - - -
318A TYR 3.5 3.4 - - - +
319A GLU* 3.7 26.7 - - + -
353A GLU* 3.3 35.2 - - + -
354A VAL* 1.3 73.1 - - - +
356A HIS* 1.3 61.0 + - - +
351P MET* 3.3 5.2 - - - +
352P GLY 2.9 38.9 + - - +
354P VAL* 4.0 13.7 - - + -
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Residues in contact with HIS 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 3.5 20.7 - - + +
31A SER* 3.0 40.8 + - - -
34A SER* 4.2 5.4 - - - -
35A ILE* 3.7 19.8 - - + +
184A LEU* 4.3 0.9 - - - -
317A HIS* 3.5 1.7 - - - +
318A TYR* 2.8 52.2 + + + +
320A LEU* 4.1 15.7 - - + -
354A VAL 4.1 0.4 + - - -
355A PHE* 1.3 74.3 - - - +
357A GLN* 1.3 60.7 + - - +
358A ALA* 4.1 4.6 - - + +
349P ALA* 3.8 18.6 - - + -
350P GLY 2.9 24.8 + - - -
351P MET* 4.0 11.2 - - - +
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Residues in contact with GLN 357 (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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180A LYS 4.4 1.6 + - - -
181A ILE* 3.7 32.9 - - + +
182A PRO* 3.9 19.4 - - - +
183A ASN* 3.3 25.9 - - - +
184A LEU* 3.8 11.3 - - + +
315A GLU* 5.9 2.9 - - + +
316A GLU 3.3 12.3 - - - +
317A HIS* 3.3 39.1 + - + +
356A HIS* 1.3 75.2 + - - +
358A ALA* 1.3 64.4 + - - +
359A MET* 6.2 0.6 - - - +
349P ALA* 3.1 4.3 - - - +
350P GLY 2.9 32.6 + - - +
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Residues in contact with ALA 358 (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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29A PHE* 3.6 37.4 - - + +
30A LEU* 3.8 13.2 - - - -
181A ILE* 4.1 2.9 - - - -
315A GLU* 3.5 1.4 - - - -
316A GLU* 2.9 32.3 + - - -
356A HIS* 4.1 4.0 - - + +
357A GLN* 1.3 77.3 - - - +
359A MET* 1.3 60.7 + - - +
348P ALA 3.3 11.0 - - - +
349P ALA* 3.9 10.1 - - + -
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Residues in contact with MET 359 (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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29A PHE* 3.2 11.9 - - - -
180A LYS* 3.9 50.5 - - + +
181A ILE* 4.1 6.7 - - + -
313A LYS* 3.8 28.5 - - - -
314A LEU 3.1 12.6 - - - +
315A GLU* 3.7 15.5 - - + +
357A GLN* 6.2 0.4 - - - +
358A ALA* 1.3 75.4 - - - +
360A VAL* 1.3 78.1 + - - +
361A ASP* 4.3 7.6 - - + +
346P GLU* 4.1 5.2 - - - +
347P ALA* 3.3 6.8 - - - -
348P ALA 2.9 45.4 + - - +
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Residues in contact with VAL 360 (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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29A PHE* 3.5 30.1 - - + -
312A PHE* 4.2 11.9 - - + -
313A LYS* 3.2 7.3 - - - +
314A LEU* 2.9 58.1 + - + +
359A MET* 1.3 79.2 - - - +
361A ASP* 1.3 63.1 + - - +
362A VAL* 3.8 12.8 - - + -
396A PHE* 4.4 3.4 - - + -
398A ILE* 4.8 4.5 - - + -
345P THR* 3.6 26.9 - - + -
346P GLU 3.3 5.8 - - - +
347P ALA* 4.0 5.6 - - + -
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Residues in contact with ASP 361 (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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311A GLN* 5.9 0.5 - - - +
312A PHE 3.6 6.4 - - - +
313A LYS* 4.0 27.8 + - + +
359A MET* 4.3 8.5 - - + -
360A VAL* 1.3 74.7 - - - +
362A VAL* 1.3 69.4 + - - +
363A ASN* 4.1 13.4 + - - +
344P ACE 4.0 0.2 - - - +
345P THR* 3.3 4.7 - - - -
346P GLU* 2.8 44.9 + - + +
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Residues in contact with VAL 362 (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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208A TRP* 4.1 13.5 - - + -
235A MET* 4.0 19.5 - - + -
264A MET* 4.1 11.2 - - + -
309A ILE* 4.4 5.8 - - + -
310A PRO 4.3 1.3 - - - +
311A GLN* 3.6 8.3 - - - +
312A PHE* 2.8 68.1 + - + +
360A VAL* 3.8 19.1 - - + -
361A ASP* 1.3 76.4 + - - +
363A ASN* 1.3 64.8 + - - +
344P ACE 3.5 8.3 - - - +
345P THR* 3.9 9.2 - - - +
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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