Contacts of the strand formed by residues 330 - 342 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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290E LEU* 3.7 35.4 - - + +
291E TYR* 3.4 7.4 - - - -
292E VAL* 2.9 46.6 + - + +
318E ASP 5.8 0.2 - - - +
328E ALA 3.6 2.8 + - - +
329E SER* 1.3 75.1 - - - +
331E ASN* 1.3 64.1 + - - +
332E GLN* 4.0 10.8 - - - +
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Residues in contact with ASN 331 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289E TYR* 2.5 32.5 + - - -
290E LEU 3.3 4.5 - - - -
291E TYR* 4.3 11.2 - - + -
330E ALA* 1.3 77.1 - - - +
332E GLN* 1.3 64.4 + - - +
359E TYR* 3.9 1.1 - - - -
360E PHE* 2.9 41.9 + - - +
361E SER* 3.4 37.6 + - - +
363E SER* 5.6 0.2 + - - -
602E C8E 3.7 14.5 + - - +
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Residues in contact with GLN 332 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288E GLN* 3.7 1.5 - - - +
289E TYR* 3.2 8.0 - - - -
290E LEU* 2.9 58.6 + - + +
315E LEU 5.4 1.4 + - - -
317E ARG 5.2 5.3 + - - -
320E THR* 5.9 1.0 + - - -
329E SER 4.7 0.3 - - - +
330E ALA* 4.0 20.8 - - - +
331E ASN* 1.3 78.3 + - - +
333E VAL* 1.3 63.4 + - - +
334E SER* 4.7 8.5 + - - +
357E ILE* 4.1 20.4 - - + +
358E TYR 3.3 12.1 - - - +
359E TYR* 3.2 36.9 + - + -
360E PHE* 4.3 1.8 - - - -
363E SER* 4.0 2.9 + - - -
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Residues in contact with VAL 333 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287E ALA* 5.2 0.7 - - + -
288E GLN 3.3 11.7 - - - +
289E TYR* 3.8 13.0 - - + -
332E GLN* 1.3 73.8 - - - +
334E SER* 1.3 64.2 + - - +
335E THR* 3.7 23.3 - - + -
356E GLN* 3.7 4.7 + - - +
357E ILE* 3.6 1.8 - - - -
358E TYR* 2.9 43.4 + - + +
360E PHE* 3.5 29.4 - - + -
602E C8E 4.1 28.9 - - + -
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Residues in contact with SER 334 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287E ALA* 3.4 1.0 - - - -
288E GLN* 2.9 43.4 + - - -
315E LEU* 2.9 29.1 + - - -
316E PHE* 3.4 23.8 - - - -
332E GLN* 4.2 7.3 + - - +
333E VAL* 1.3 71.8 - - - +
335E THR* 1.3 61.7 + - - +
356E GLN 3.4 9.4 - - - -
357E ILE* 3.6 17.1 - - - +
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Residues in contact with THR 335 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286E ARG 3.3 6.1 - - - -
287E ALA* 4.5 11.0 - - + -
315E LEU* 4.8 0.7 - - - +
316E PHE* 4.0 5.5 - - - -
333E VAL* 3.7 20.0 - - + -
334E SER* 1.3 78.3 - - - +
336E GLY* 1.3 59.6 + - - +
355E GLY* 3.1 2.4 - - - -
356E GLN* 2.7 63.7 + - - +
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Residues in contact with GLY 336 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284E GLU 3.8 0.8 - - - +
285E PRO* 3.5 3.1 - - - +
286E ARG* 2.9 36.1 + - - +
312E TYR* 3.6 15.9 - - - -
316E PHE* 3.9 6.9 - - - -
335E THR* 1.3 76.3 - - - +
337E LEU* 1.3 61.0 + - - +
338E THR 4.4 0.4 - - - -
354E VAL 3.4 10.3 - - - -
355E GLY* 3.9 2.2 - - - -
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Residues in contact with LEU 337 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283E LEU* 3.8 37.9 - - + -
284E GLU 3.6 18.2 - - - +
285E PRO* 3.7 12.6 - - + -
312E TYR* 3.7 1.0 + - - -
336E GLY* 1.3 74.3 - - - +
338E THR* 1.3 70.9 + - - +
339E SER* 5.1 1.1 - - - +
352E VAL 3.8 0.9 - - - +
353E SER* 3.3 4.5 - - - -
354E VAL* 2.9 37.7 + - + +
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Residues in contact with THR 338 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283E LEU* 3.8 0.4 - - - -
284E GLU* 2.9 55.5 + - - +
312E TYR* 3.3 20.6 + - - -
337E LEU* 1.3 74.1 - - - +
339E SER* 1.3 60.7 + - - +
340E ARG* 3.9 29.2 - - + +
351E ASN* 3.8 16.6 - - - +
352E VAL 3.4 2.2 - - - -
353E SER* 3.0 23.7 + - - +
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Residues in contact with SER 339 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281E GLN* 3.5 25.6 + - - +
282E THR 3.1 15.0 + - - -
283E LEU* 4.2 16.2 - - - +
337E LEU* 4.2 2.1 - - - +
338E THR* 1.3 73.7 - - - +
340E ARG* 1.3 62.7 + - - +
341E ILE* 5.5 0.7 - - - +
350E PHE* 4.8 2.8 - - - -
351E ASN* 3.6 3.6 + - - -
352E VAL* 3.0 47.1 + - - +
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Residues in contact with ARG 340 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266E LYS* 6.1 0.4 - - - +
280E THR 4.4 0.2 - - - -
281E GLN* 3.3 3.3 - - - +
282E THR* 2.9 40.7 + - - +
284E GLU* 3.3 27.7 + - - +
338E THR* 3.9 20.0 - - + +
339E SER* 1.3 77.8 - - - +
341E ILE* 1.3 71.4 + - - +
342E TYR* 3.6 28.5 - - + -
348E GLU* 2.6 37.2 + - + +
350E PHE* 3.7 7.9 - - - +
351E ASN* 3.7 14.1 - - - +
137F ARG* 3.5 40.5 - - - +
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Residues in contact with ILE 341 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273E MET* 4.6 23.8 - - + -
279E PHE* 4.2 14.6 - - + -
280E THR 3.4 4.5 - - - +
281E GLN* 4.0 21.5 - - + +
339E SER* 5.5 0.9 - - - +
340E ARG* 1.3 81.4 - - - +
342E TYR* 1.3 73.2 + - - +
348E GLU* 3.7 2.6 - - - -
349E ARG* 2.9 29.4 + - + -
350E PHE* 3.2 37.4 + - + +
604E C8E 4.5 26.9 - - - +
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Residues in contact with TYR 342 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279E PHE* 3.2 12.7 - - - +
280E THR* 2.9 40.3 + - + +
282E THR* 3.7 25.4 - - + -
284E GLU* 5.1 1.2 + - - -
340E ARG* 3.6 30.9 - - + -
341E ILE* 1.3 76.2 - - - +
343E ASP* 1.3 61.3 + - - +
346E ARG* 3.8 45.8 - - + +
347E VAL 3.4 4.5 - - - +
348E GLU* 3.9 24.9 + - + -
349E ARG* 5.1 0.4 - - - -
10F VAL* 5.0 14.7 - - + +
137F ARG* 4.0 23.4 + - + +
140F LEU* 5.7 10.1 - - + -
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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