Contacts of the strand formed by residues 330 - 342 (chain A) in PDB entry 5IXM
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 330 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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290A LEU* 3.6 39.0 - - + +
291A TYR* 3.3 6.1 - - - -
292A VAL* 2.8 43.2 + - + +
318A ASP 5.8 0.4 - - - +
328A ALA 4.6 1.8 - - - +
329A SER* 1.3 76.2 - - - +
331A ASN* 1.3 64.5 + - - +
332A GLN* 4.0 11.4 - - - +
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Residues in contact with ASN 331 (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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289A TYR* 2.5 32.5 + - - -
290A LEU 3.2 4.7 - - - -
291A TYR* 3.8 16.8 - - + -
330A ALA* 1.3 75.9 - - - +
332A GLN* 1.3 64.8 + - - +
359A TYR* 4.1 1.0 - - - -
360A PHE* 3.0 34.0 + - - +
361A SER* 3.3 29.9 + - - +
363A SER* 5.7 0.4 + - - -
605A C8E 3.5 37.8 + - - +
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Residues in contact with GLN 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A GLN 3.6 0.5 - - - +
289A TYR* 3.3 6.8 - - - -
290A LEU* 2.9 57.2 + - + +
315A LEU 5.5 1.2 + - - -
317A ARG 5.3 4.8 + - - -
320A THR* 5.9 1.2 + - - -
330A ALA* 4.0 15.1 - - - +
331A ASN* 1.3 84.4 + - - +
333A VAL* 1.3 65.1 + - - +
334A SER* 4.7 7.5 + - - +
357A ILE* 4.2 21.1 - - + +
358A TYR 3.3 14.4 - - - +
359A TYR* 3.2 36.2 + - + -
360A PHE* 4.1 2.5 - - - -
363A SER* 4.0 3.5 + - - -
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Residues in contact with VAL 333 (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 GLN 3.2 12.3 - - - +
289A TYR* 3.7 10.5 - - + -
332A GLN* 1.3 73.6 - - - +
334A SER* 1.3 64.1 + - - +
335A THR* 3.6 25.7 + - + -
356A GLN* 4.0 1.6 - - - +
357A ILE* 3.6 1.2 - - - -
358A TYR* 2.9 44.2 + - + +
360A PHE* 3.4 28.9 - - + -
603A C8E 3.6 41.3 - - - +
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Residues in contact with SER 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A ALA* 3.5 0.7 - - - -
288A GLN* 2.9 52.3 + - - -
315A LEU* 3.0 28.0 + - - -
316A PHE* 3.4 16.0 - - - -
332A GLN* 4.2 7.7 + - - +
333A VAL* 1.3 72.0 - - - +
335A THR* 1.3 61.9 + - - +
356A GLN 3.3 9.0 - - - -
357A ILE* 3.4 18.2 - - - +
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Residues in contact with THR 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A ARG 3.3 5.4 - - - -
287A ALA* 4.2 14.6 - - + -
316A PHE* 4.0 5.9 - - - -
333A VAL* 3.6 21.9 + - + +
334A SER* 1.3 79.5 - - - +
336A GLY* 1.3 57.4 + - - +
355A GLY* 3.2 1.4 - - - -
356A GLN* 2.7 63.4 + - - +
606C C8E 5.7 4.9 - - + -
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Residues in contact with GLY 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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284A GLU 3.9 1.1 - - - +
285A PRO* 3.5 2.9 - - - +
286A ARG* 2.9 35.6 + - - +
312A TYR* 3.8 13.9 - - - -
316A PHE* 3.9 6.6 - - - -
335A THR* 1.3 76.4 - - - +
337A LEU* 1.3 60.6 + - - +
354A VAL 3.4 9.4 - - - -
355A GLY* 3.8 3.8 - - - -
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Residues in contact with LEU 337 (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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283A LEU* 3.7 40.4 - - + -
284A GLU 3.6 1.6 - - - -
285A PRO* 3.9 24.5 - - + -
312A TYR* 3.9 1.2 + - - -
336A GLY* 1.3 74.8 - - - +
338A THR* 1.3 66.6 + - - +
339A SER* 4.2 1.7 + - - +
352A VAL 3.8 1.0 - - - +
353A SER* 3.3 3.3 - - - -
354A VAL* 2.8 38.3 + - + +
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Residues in contact with THR 338 (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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282A THR 3.7 0.2 - - - +
283A LEU* 4.8 0.2 - - - -
284A GLU* 2.9 56.9 + - - +
312A TYR* 3.4 19.9 + - - -
337A LEU* 1.3 74.9 - - - +
339A SER* 1.3 60.7 + - - +
340A ARG* 3.9 27.4 - - + +
351A ASN* 3.8 16.2 - - - +
352A VAL 3.4 2.9 - - - -
353A SER* 3.2 23.5 + - - +
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Residues in contact with SER 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A GLN* 3.4 27.5 + - - +
282A THR 3.0 14.7 + - - -
283A LEU* 4.4 14.8 - - - +
337A LEU* 4.2 2.3 + - - +
338A THR* 1.3 72.6 - - - +
340A ARG* 1.3 63.2 + - - +
341A ILE* 5.4 0.9 - - - +
350A PHE* 4.9 2.4 - - - -
351A ASN* 3.5 3.6 + - - -
352A VAL* 2.9 48.8 + - - +
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Residues in contact with ARG 340 (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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266A LYS* 5.3 3.2 - - - +
280A THR 4.3 0.7 - - - -
281A GLN* 3.3 6.6 - - - +
282A THR* 2.9 39.4 + - - +
284A GLU* 2.9 33.5 + - - +
338A THR* 3.9 15.0 - - + +
339A SER* 1.3 80.1 - - - +
341A ILE* 1.3 67.1 + - - +
342A TYR* 3.4 31.2 + - + -
348A GLU* 2.8 35.4 + - - +
350A PHE* 3.6 7.9 - - - +
351A ASN* 3.6 13.9 - - - +
137B ARG* 3.3 43.4 - - - +
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Residues in contact with ILE 341 (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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273A MET* 4.2 23.8 - - + -
279A PHE* 4.2 15.3 - - + -
280A THR 3.2 6.3 - - - +
281A GLN* 4.1 19.3 - - + +
339A SER* 5.4 0.7 - - - +
340A ARG* 1.3 80.7 - - - +
342A TYR* 1.3 75.0 + - - +
348A GLU* 3.7 2.3 - - - -
349A ARG* 2.9 27.5 + - + -
350A PHE* 3.0 40.0 + - + +
602A C8E 4.4 28.7 - - - +
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Residues in contact with TYR 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A PHE* 3.2 12.1 - - - +
280A THR* 2.9 38.1 + - - +
282A THR* 3.5 32.3 - - + -
284A GLU* 4.9 0.3 + - - -
340A ARG* 3.4 31.5 - - + -
341A ILE* 1.3 77.3 - - - +
343A ASP* 1.3 65.7 + - - +
346A ARG* 4.1 32.3 - - - +
347A VAL 3.3 5.4 - - - +
348A GLU* 3.8 32.0 + - + -
349A ARG* 5.0 0.2 - - - -
9B GLN* 3.7 19.9 + - - -
137B ARG* 4.1 20.3 + - + +
140B LEU* 4.2 17.2 - - + +
141B THR* 6.1 2.0 - - + -
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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