Contacts of the strand formed by residues 325 - 335 (chain A) in PDB entry 4P0S
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 GLU 325 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260A LEU* 4.2 3.2 - - - +
301A ARG* 2.6 47.8 + - - -
311A VAL* 5.0 12.3 - - + -
312A ALA 3.6 3.4 - - - -
313A GLN* 4.0 22.4 + - + -
323A PRO* 3.4 20.6 + - - +
324A GLY* 1.4 73.7 - - - +
326A LEU* 1.3 60.7 + - - +
455A THR* 3.3 7.1 - - - -
456A PHE* 2.6 55.1 + - + +
457A SER* 5.4 1.6 + - - -
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Residues in contact with LEU 326 (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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260A LEU* 4.0 17.0 - - + -
262A LEU* 3.5 31.9 - - + -
311A VAL* 3.0 6.3 - - - -
312A ALA* 2.6 45.8 + - + +
325A GLU* 1.3 81.4 - - - +
327A VAL* 1.3 57.3 + - - +
328A LEU* 5.1 0.2 - - - -
428A LEU* 4.7 3.8 - - + -
429A ARG* 4.0 13.2 - - - +
430A SER* 4.0 31.0 - - - +
453A LEU* 4.4 14.8 - - + +
454A LEU 3.2 8.1 - - - +
455A THR* 3.7 25.1 - - + -
456A PHE 4.7 0.2 - - - -
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Residues in contact with VAL 327 (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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309A VAL* 4.0 16.8 - - + -
310A TRP 3.1 15.9 - - - +
311A VAL* 3.9 10.1 - - + -
325A GLU 4.3 0.4 + - - -
326A LEU* 1.3 71.1 - - - +
328A LEU* 1.3 73.7 + - - +
361A LEU* 3.9 28.6 - - + +
453A LEU* 3.5 19.4 - - - +
454A LEU* 2.9 41.8 + - + +
455A THR 4.4 2.2 - - - +
456A PHE* 4.5 4.4 - - - +
459A PHE* 4.3 17.9 - - + -
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Residues in contact with LEU 328 (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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269A VAL* 4.4 11.2 - - + -
310A TRP* 2.4 43.9 + - + +
311A VAL 4.1 1.3 - - - +
312A ALA* 4.0 26.2 - - + +
327A VAL* 1.3 84.5 - - - +
329A ASP* 1.3 65.7 + - - +
330A HIS* 3.2 9.6 + - - +
361A LEU* 3.6 7.6 - - - +
419A LEU* 3.7 35.4 - - + -
423A TYR* 3.9 32.8 - - + +
428A LEU* 6.1 0.7 - - + -
453A LEU* 3.9 18.2 - - + -
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Residues in contact with ASP 329 (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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328A LEU* 1.3 75.9 - - - +
330A HIS* 1.3 64.6 + - - +
360A GLY 4.4 2.8 - - - +
361A LEU* 3.9 12.3 - - - +
362A GLU* 3.1 30.2 + - - +
363A ARG* 3.0 51.5 + - + +
423A TYR* 4.6 4.4 + - - +
431A ARG* 5.1 1.4 + - - -
447A PRO 5.3 1.4 - - - -
448A ASN* 4.0 8.1 - - - +
450A LEU* 3.1 42.8 - - + +
453A LEU* 4.2 6.8 - - + +
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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
----------------------------------------------------------
309A VAL* 4.1 0.2 - - - -
310A TRP* 3.7 41.8 + - + -
328A LEU* 3.2 10.0 - - - +
329A ASP* 1.3 87.0 + - + +
331A ILE* 1.3 63.6 + - - +
361A LEU* 3.7 4.7 - - - +
363A ARG* 3.4 27.5 + - + +
365A VAL* 4.4 18.8 - - + -
415A LEU* 5.0 2.9 - - + -
419A LEU* 4.4 12.8 - - + +
448A ASN* 3.6 27.1 - - - -
416B GLN* 3.5 15.3 + - + -
417B LEU* 3.3 36.1 - - + +
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Residues in contact with ILE 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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305A VAL 4.1 17.9 - - - +
306A GLY* 4.4 8.3 - - - -
308A PHE 3.1 17.7 - - - +
309A VAL* 3.5 17.0 - - + +
310A TRP* 5.2 0.2 - - - -
330A HIS* 1.3 76.2 - - - +
332A VAL* 1.3 68.2 + - - +
356A LEU* 4.8 11.0 - - + +
359A CYS* 4.4 11.7 - - - -
361A LEU* 3.5 26.2 - - + +
363A ARG 3.1 12.4 + - - +
364A ARG* 4.1 17.9 - - + -
365A VAL* 2.8 28.6 + - - +
459A PHE* 4.3 6.3 - - + -
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Residues in contact with VAL 332 (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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306A GLY* 5.4 0.2 - - - -
307A ASP 3.4 4.2 + - - -
308A PHE* 2.7 62.9 + - + +
310A TRP* 4.5 14.8 - - + -
331A ILE* 1.3 78.6 - - - +
333A GLU* 1.3 64.0 + - - +
365A VAL* 3.1 26.9 - - + +
367A LEU* 3.3 36.1 - - + +
411A TYR* 5.8 0.4 - - + -
412A LEU* 4.9 4.9 - - + -
415A LEU* 4.4 17.5 - - + -
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Residues in contact with GLU 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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306A GLY* 3.4 26.5 + - - -
307A ASP* 3.3 24.9 - - - +
332A VAL* 1.3 73.0 - - - +
334A ARG* 1.3 61.1 + - - +
335A LYS* 4.0 5.1 + - + -
352A GLN* 2.4 39.4 + - - +
356A LEU* 4.7 11.8 - - + +
365A VAL 3.2 6.4 + - - +
366A TYR* 3.4 48.7 - - + +
367A LEU 3.2 22.6 + - - +
55L T 5.4 1.9 + - - -
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Residues in contact with ARG 334 (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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277A GLU* 2.8 52.4 + - - +
287A LEU* 6.4 0.2 - - - -
307A ASP* 3.2 22.4 + - - +
308A PHE* 3.5 34.4 - - + -
332A VAL 4.1 1.4 - - - -
333A GLU* 1.3 68.6 - - - +
335A LYS* 1.3 79.1 + - - +
336A ARG* 4.0 20.8 - - - +
339A ASP* 5.9 1.0 + - - -
367A LEU* 3.3 20.0 - - + +
369A GLU* 3.1 30.0 + - + +
405A ILE* 3.8 19.8 - - - +
408A SER* 5.7 3.8 - - - -
55L T 5.9 0.6 + - - -
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Residues in contact with LYS 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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277A GLU* 5.8 1.2 + - - -
307A ASP* 4.8 2.8 + - - -
333A GLU* 4.0 7.1 + - + +
334A ARG* 1.3 87.4 + - - +
336A ARG* 1.3 71.3 + - - +
337A LEU* 5.4 0.2 - - - +
339A ASP* 4.1 15.5 + - + +
340A LEU* 4.2 22.4 - - + +
343A SER* 3.4 23.8 - - - -
348A ARG* 3.4 15.8 - - - +
352A GLN* 3.2 35.9 + - - +
366A TYR* 4.3 18.6 - - + +
367A LEU 3.0 9.0 + - - +
368A VAL* 3.7 6.6 - - + +
369A GLU* 2.8 27.0 + - - +
55L T 4.5 11.1 + - - -
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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