Contacts of the helix formed by residues 316 - 333 (chain A) in PDB entry 4DVQ
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 VAL 316 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A PHE* 3.9 7.4 - - + -
196A THR* 3.4 17.6 + - - +
197A ILE* 3.8 19.1 - - + -
200A SER* 5.7 0.4 - - - -
223A PHE* 3.8 26.5 - - + -
224A LEU* 3.7 30.3 - - + -
227A LEU* 4.2 4.7 - - + -
312A THR 3.9 11.2 - - - +
313A ALA 4.3 1.5 + - - +
314A GLY 3.5 1.6 + - - -
315A SER* 1.3 86.0 - - - +
317A ASP* 1.3 70.9 + - - +
318A THR 3.3 1.1 - - - -
319A THR* 3.4 2.1 + - - -
320A ALA* 2.8 30.4 + - - +
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Residues in contact with ASP 317 (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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193A PHE* 3.7 25.0 - - - -
224A LEU* 5.2 2.7 - - - +
227A LEU* 3.3 33.9 - - - +
228A GLU* 5.2 4.5 + - - +
231A PHE* 3.9 26.2 - - + -
313A ALA 4.9 2.2 + - - +
314A GLY 5.3 0.2 - - - -
316A VAL* 1.3 73.7 - - - +
318A THR* 1.3 67.0 + - + +
321A PHE* 3.1 41.3 + - + +
378A VAL* 4.7 0.3 - - - +
488A ILE* 3.8 20.7 - - + +
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Residues in contact with THR 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A PHE* 5.8 0.4 - - + -
314A GLY 2.7 30.7 + - - +
315A SER* 4.0 0.5 - - - -
316A VAL 3.9 2.4 + - - -
317A ASP* 1.3 74.1 - - + +
319A THR* 1.3 64.5 + - - +
322A PRO* 2.9 25.5 - - - +
378A VAL* 3.2 24.6 - - + +
488A ILE* 4.8 4.0 - - + -
601A HEM 3.4 31.7 - - + +
602A 1CA 4.1 37.9 - - + -
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Residues in contact with THR 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A THR* 3.8 18.2 - - + -
315A SER 4.4 4.1 + - - -
316A VAL 3.4 5.5 + - - -
318A THR* 1.3 83.5 + - - +
320A ALA* 1.3 66.8 + - - +
321A PHE 3.2 2.6 + - - -
322A PRO* 3.5 4.4 - - - +
323A LEU* 3.3 20.1 + - + +
456A ALA* 3.8 28.9 - - - +
459A GLU* 4.0 17.9 + - + +
460A MET* 3.9 24.3 - - + +
601A HEM 4.0 11.3 - - - +
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Residues in contact with ALA 320 (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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192A ILE* 3.6 9.1 - - + +
193A PHE* 3.6 40.8 - - + -
196A THR* 3.8 17.7 - - + +
316A VAL 2.8 22.5 + - - +
317A ASP 3.3 0.4 + - - +
319A THR* 1.3 74.8 - - - +
321A PHE* 1.3 57.9 + - - +
323A LEU* 3.4 3.8 - - - +
324A LEU* 3.1 32.0 + - - +
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Residues in contact with PHE 321 (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 GLN* 4.0 16.6 - - - -
193A PHE* 3.5 33.9 - + - -
317A ASP* 3.1 25.4 + - + +
320A ALA* 1.3 75.3 - - - +
322A PRO* 1.3 74.3 - - + +
324A LEU* 3.2 8.5 + - + +
325A MET* 3.0 29.1 + - - +
378A VAL* 5.2 2.9 - - + -
488A ILE* 3.4 31.6 - - + -
489A LEU 5.0 5.6 - - - +
490A ARG* 3.5 31.0 - - + -
491A PRO* 3.7 33.4 - - + -
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Residues in contact with PRO 322 (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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318A THR 2.9 29.8 - - - +
319A THR 3.5 4.5 - - - +
321A PHE* 1.3 93.6 - - + +
323A LEU* 1.3 51.5 + - - +
325A MET* 3.4 2.4 + - + -
326A THR* 2.6 38.5 + - - -
369A LEU* 5.8 0.7 - - + -
372A THR* 3.3 14.2 - - + +
373A LEU* 4.0 16.4 - - + -
376A TYR 5.2 2.0 - - - +
378A VAL* 3.1 22.2 - - + -
460A MET* 4.0 16.4 - - + -
601A HEM 4.0 9.2 - - + -
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Residues in contact with LEU 323 (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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192A ILE* 3.9 23.1 - - + -
195A TYR* 4.0 29.2 - - + -
196A THR* 4.4 5.8 - - + -
319A THR* 3.3 11.0 + - + +
320A ALA 3.4 8.5 - - - +
322A PRO* 1.3 74.8 - - - +
324A LEU* 1.3 66.6 + - - +
326A THR* 3.3 5.1 + - - -
327A LEU* 2.9 29.0 + - + +
369A LEU* 5.9 0.2 - - - -
460A MET* 3.6 46.6 - - + +
463A LEU* 4.0 14.4 - - + -
464A LEU* 3.7 24.7 - - + -
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Residues in contact with LEU 324 (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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188A VAL* 4.0 27.1 - - + -
189A GLN* 4.1 27.8 - - + +
192A ILE* 3.8 25.1 - - + -
193A PHE* 4.2 13.5 - - + -
320A ALA 3.1 29.9 + - - +
321A PHE* 3.2 17.2 + - + +
323A LEU* 1.3 74.6 - - - +
325A MET* 1.3 70.2 + - + +
327A LEU* 3.2 7.6 + - + +
328A PHE* 2.8 28.4 + - - +
491A PRO* 5.2 2.2 - - + -
494A SER* 4.9 6.7 - - - +
495A PRO* 6.1 3.8 - - + -
497A LEU* 5.3 1.8 - - + +
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Residues in contact with MET 325 (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 PHE 3.0 21.3 + - - +
322A PRO* 3.8 4.7 - - + +
323A LEU 3.3 0.2 - - - -
324A LEU* 1.3 86.6 - - + +
326A THR* 1.3 52.7 + - - +
328A PHE* 3.6 8.5 - - + +
329A GLU* 2.7 38.6 + - - +
372A THR* 3.8 8.1 - - + -
376A TYR* 3.7 40.4 - - + -
481A ILE* 3.9 24.7 - - + -
483A MET* 4.2 12.6 - - + +
491A PRO* 3.9 40.4 - - + -
493A THR 5.2 1.1 - - - +
495A PRO* 5.3 3.6 - - + -
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Residues in contact with THR 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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322A PRO 2.6 24.1 + - - -
323A LEU* 3.5 5.2 - - - -
325A MET* 1.3 74.5 - - - +
327A LEU* 1.3 60.6 + - - +
329A GLU* 3.3 1.1 + - - +
330A LEU* 2.8 47.0 + - + +
365A LEU* 5.7 0.2 - - + -
368A ALA* 4.9 5.8 - - + -
369A LEU* 4.0 12.2 - - + +
372A THR* 2.7 20.3 + - - +
423A TYR* 3.6 18.6 - - - +
464A LEU* 3.7 29.2 - - + -
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Residues in contact with LEU 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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168A PHE* 6.5 0.2 - - + -
188A VAL* 4.4 15.3 - - + -
192A ILE* 4.1 30.7 - - + -
323A LEU* 2.9 19.8 + - + +
324A LEU* 3.5 8.7 - - + +
326A THR* 1.3 74.9 - - - +
328A PHE* 1.3 64.3 + - - +
330A LEU* 3.3 8.9 + - + +
331A ALA* 3.0 23.6 + - - +
463A LEU* 4.9 4.9 - - + -
464A LEU* 3.5 24.0 - - + -
467A VAL* 4.8 13.5 - - + -
473A VAL* 4.4 10.6 - - + +
497A LEU* 3.8 14.8 - - + -
499A PHE* 4.5 23.3 - - + -
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Residues in contact with PHE 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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324A LEU 2.8 16.7 + - - +
325A MET* 3.6 18.6 - - + +
327A LEU* 1.3 76.4 - - - +
329A GLU* 1.3 70.9 + - + +
331A ALA* 3.4 5.9 + - + +
332A ARG* 3.2 63.5 + - + +
376A TYR* 4.7 5.2 - - - -
475A THR* 5.1 3.1 - - - -
477A THR* 3.3 24.5 - - + -
479A GLU 3.6 17.5 - - - -
481A ILE* 3.6 31.9 - - + -
495A PRO* 3.7 26.5 - - + -
497A LEU* 4.6 9.1 - - + +
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Residues in contact with GLU 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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325A MET 2.7 22.7 + - - +
326A THR 3.9 1.6 - - - +
328A PHE* 1.3 74.9 - - + +
330A LEU* 1.3 59.4 + - - +
332A ARG* 2.8 27.0 + - - -
333A ASN* 2.8 53.4 + - - +
375A LEU* 4.3 5.2 - - - +
376A TYR* 2.6 38.3 + - + -
423A TYR* 3.5 48.3 - - + +
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Residues in contact with LEU 330 (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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326A THR* 2.8 37.9 + - + +
327A LEU* 3.7 8.1 - - + +
329A GLU* 1.3 73.7 - - - +
331A ALA* 1.3 63.5 + - - +
333A ASN 3.1 21.2 + - - +
334A PRO 3.6 0.2 - - - -
336A VAL* 4.3 3.1 - - + -
337A GLN* 3.2 34.3 - - + +
340A LEU* 3.4 35.2 - - + -
365A LEU* 5.2 2.2 - - + -
423A TYR* 4.2 19.5 - - + +
464A LEU* 5.0 9.4 - - + -
468A LEU* 4.1 29.4 - - + -
473A VAL* 5.6 3.6 - - + -
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Residues in contact with ALA 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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327A LEU 3.0 16.4 + - - +
328A PHE* 3.7 6.1 - - + +
329A GLU 3.4 0.2 - - - -
330A LEU* 1.3 75.8 - - - +
332A ARG* 1.3 59.4 + - - +
333A ASN 3.7 0.2 + - - -
334A PRO* 3.8 10.6 - - - +
337A GLN* 4.0 0.2 + - - -
473A VAL* 3.4 27.8 - - + +
474A GLU* 3.8 12.9 - - - +
475A THR* 3.2 30.6 + - - +
478A GLN* 4.7 4.9 + - - +
497A LEU* 4.0 8.1 - - + -
280E PHE* 5.8 3.3 - - - -
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Residues in contact with ARG 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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328A PHE* 3.3 38.0 - - + +
329A GLU* 2.8 41.4 + - - +
331A ALA* 1.3 77.1 - - - +
333A ASN* 1.3 65.5 + - - +
334A PRO* 3.3 10.0 - - - +
376A TYR* 3.9 4.9 + - - -
421A GLU 5.9 0.6 + - - -
475A THR* 6.3 0.2 - - - -
478A GLN* 3.0 52.8 + - + +
480A ASP* 2.3 53.7 + - - +
106G LEU* 5.3 1.9 - - - +
107G HIS* 5.6 0.7 + - - -
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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
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329A GLU* 2.8 47.2 + - - +
330A LEU* 3.2 6.3 - - - +
332A ARG* 1.3 88.9 + - - +
334A PRO* 1.4 59.3 - - - +
335A ASP* 3.2 14.1 - - - +
336A VAL* 2.9 20.0 + - + +
337A GLN 2.9 23.0 + - - -
422A ARG* 6.0 0.9 - - - +
423A TYR* 4.0 23.5 + - + +
106G LEU* 5.4 0.4 - - - -
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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
------------------------------------------------------------
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