Contacts of the helix formed by residues 316 - 333 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193I PHE* 3.9 8.3 - - + -
196I THR* 3.2 18.3 + - - +
197I ILE* 3.8 23.8 - - + -
200I SER* 5.7 0.7 - - - -
223I PHE* 3.7 27.4 - - + -
224I LEU* 3.5 31.9 - - + -
227I LEU* 4.0 12.1 - - + -
312I THR 3.8 12.1 - - - +
313I ALA 4.2 2.2 + - - +
314I GLY 3.4 2.6 - - - -
315I SER* 1.3 81.9 - - - +
317I ASP* 1.3 67.6 + - - +
318I THR 3.4 0.9 - - - -
319I THR 3.6 1.4 + - - -
320I ALA* 3.2 20.7 + - - +
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Residues in contact with ASP 317 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193I PHE* 3.3 30.3 - - + -
224I LEU* 5.1 2.8 - - - +
227I LEU* 3.4 33.1 - - - +
228I GLU* 5.1 4.7 + - - +
231I PHE* 3.5 26.2 - - + -
313I ALA 4.7 2.0 + - - +
314I GLY 5.0 0.6 + - - -
316I VAL* 1.3 77.6 - - - +
318I THR* 1.3 66.9 + - - +
321I PHE* 3.3 35.7 + - + +
378I VAL* 4.7 0.3 - - - +
488I ILE* 3.6 23.3 - - + +
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Residues in contact with THR 318 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231I PHE* 6.1 0.4 - - + -
314I GLY 2.6 29.9 + - - +
315I SER 3.9 1.6 - - - -
317I ASP* 1.3 77.7 - - + +
319I THR* 1.3 71.8 + - - -
322I PRO* 2.9 26.3 - - - +
378I VAL* 3.5 25.7 - - + +
488I ILE* 5.0 2.4 - - + +
601I HEM 3.5 29.8 - - + +
602I 1CA 4.1 35.9 - - + -
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Residues in contact with THR 319 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196I THR* 4.2 13.0 - - + -
315I SER 3.5 14.6 + - - -
316I VAL 3.6 1.0 + - - -
317I ASP 3.3 0.4 - - - -
318I THR* 1.3 84.6 + - - +
320I ALA* 1.3 66.1 + - - +
321I PHE 3.3 0.4 - - - -
322I PRO* 3.3 5.7 - - - +
323I LEU* 3.2 20.3 + - + +
456I ALA* 3.7 18.6 - - - +
459I GLU* 4.0 18.7 + - + +
460I MET* 3.4 28.7 - - + +
601I HEM 3.7 17.2 - - - +
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Residues in contact with ALA 320 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192I ILE* 3.8 9.0 - - + +
193I PHE* 3.5 38.1 - - + -
196I THR* 3.8 18.8 - - + +
316I VAL 3.2 19.5 + - - +
317I ASP 3.4 0.2 + - - -
319I THR* 1.3 78.4 - - - +
321I PHE* 1.3 57.3 + - - +
323I LEU* 3.1 5.0 + - - +
324I LEU* 2.8 32.3 + - - +
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Residues in contact with PHE 321 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189I GLN* 4.0 18.2 - - - -
193I PHE* 3.5 30.3 - + - -
317I ASP* 3.3 24.2 + - + +
320I ALA* 1.3 78.6 - - - +
322I PRO* 1.3 66.5 - - + +
324I LEU* 3.4 12.7 + - + +
325I MET* 2.9 34.6 + - + +
378I VAL* 5.5 2.7 - - + -
488I ILE* 4.1 16.4 - - + -
489I LEU 4.9 7.6 - - - +
490I ARG* 3.5 36.1 - - + -
491I PRO* 3.2 38.1 - - + -
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Residues in contact with PRO 322 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318I THR 2.9 30.1 - - - +
319I THR 3.3 4.0 - - - +
321I PHE* 1.3 89.6 - - + +
323I LEU* 1.3 55.5 + - - +
325I MET* 4.3 1.8 - - + -
326I THR* 2.6 38.3 + - - -
372I THR* 3.5 11.8 - - + +
373I LEU* 3.8 14.8 - - + -
376I TYR* 5.3 3.4 - - + +
378I VAL* 3.3 23.1 - - + -
460I MET* 3.5 22.2 - - + -
601I HEM 4.3 3.4 - - + -
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Residues in contact with LEU 323 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192I ILE* 4.0 18.8 - - + -
195I TYR* 3.9 33.0 - - + -
196I THR* 4.2 9.6 - - + -
319I THR* 3.2 7.6 + - + +
320I ALA 3.1 9.0 + - - +
322I PRO* 1.3 75.8 - - - +
324I LEU* 1.3 64.9 + - - +
326I THR* 2.9 8.1 + - - -
327I LEU* 2.9 27.8 + - + +
459I GLU 4.8 0.2 - - - -
460I MET* 3.7 40.5 - - + +
463I LEU* 3.5 28.5 - - + -
464I LEU* 3.7 14.8 - - + -
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Residues in contact with LEU 324 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188I VAL* 4.0 18.8 - - + -
189I GLN* 3.7 46.4 - - + +
192I ILE* 4.2 11.6 - - + +
193I PHE* 3.9 27.1 - - + -
320I ALA 2.8 19.0 + - - +
321I PHE* 3.5 15.7 - - + +
323I LEU* 1.3 75.3 - - - +
325I MET* 1.3 70.0 + - + +
327I LEU* 3.1 9.2 + - - +
328I PHE* 2.9 27.2 + - - +
491I PRO* 5.6 1.1 - - + -
494I SER* 4.3 7.9 - - - +
495I PRO* 5.8 3.7 - - + +
497I LEU* 5.1 2.7 - - + +
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Residues in contact with MET 325 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321I PHE* 2.9 23.2 + - + +
322I PRO* 4.3 0.7 - - + -
323I LEU 3.2 0.2 - - - -
324I LEU* 1.3 87.6 - - + +
326I THR* 1.3 57.1 + - - +
328I PHE* 3.6 15.8 - - + +
329I GLU* 3.0 32.6 + - - +
372I THR* 3.8 11.2 - - + -
376I TYR* 3.7 42.2 - - + -
481I ILE* 4.7 15.7 - - + -
483I MET* 4.5 9.6 - - + +
491I PRO* 3.8 39.5 - - + -
493I THR 4.9 3.4 - - - +
494I SER* 6.2 0.2 - - - -
495I PRO* 5.3 6.7 - - + -
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Residues in contact with THR 326 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322I PRO 2.6 26.2 + - - -
323I LEU* 2.9 7.4 + - - -
325I MET* 1.3 70.1 - - - +
327I LEU* 1.3 60.5 + - - +
329I GLU* 3.3 1.1 + - - +
330I LEU* 2.9 48.0 + - + +
365I LEU* 5.7 0.4 - - + -
368I ALA* 4.7 5.2 - - + -
369I LEU* 4.0 15.0 - - + +
372I THR* 3.0 16.9 + - - +
423I TYR* 3.4 21.5 - - - +
460I MET* 4.4 0.2 - - - +
464I LEU* 3.7 28.3 - - + -
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Residues in contact with LEU 327 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168I PHE* 6.3 0.4 - - + -
188I VAL* 4.7 4.7 - - + -
192I ILE* 4.1 31.6 - - + -
323I LEU 2.9 19.0 + - - +
324I LEU* 3.1 10.0 + - - +
326I THR* 1.3 72.9 - - - +
328I PHE* 1.3 66.0 + - - +
330I LEU* 3.4 8.5 + - + +
331I ALA* 3.1 23.2 + - - +
463I LEU* 4.5 8.3 - - + -
464I LEU* 3.8 21.3 - - + -
467I VAL* 4.4 14.8 - - + -
473I VAL* 4.1 15.4 - - + +
497I LEU* 3.8 15.3 - - + -
499I PHE* 4.3 29.8 - - + -
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Residues in contact with PHE 328 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324I LEU 2.9 15.9 + - - +
325I MET* 3.6 18.4 - - + +
327I LEU* 1.3 77.1 - - - +
329I GLU* 1.3 66.3 + - + +
331I ALA* 3.2 4.0 + - - +
332I ARG* 3.0 71.9 + - + +
376I TYR* 4.6 5.8 - - - -
475I THR* 4.9 2.2 - - - -
477I THR* 3.3 20.9 - - + -
479I GLU 3.4 18.2 - - - -
481I ILE* 3.7 29.8 - - + -
495I PRO* 3.6 30.7 - - + -
497I LEU* 4.3 12.9 - - + +
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Residues in contact with GLU 329 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325I MET 3.0 21.1 + - - +
326I THR 3.3 1.5 + - - +
328I PHE* 1.3 79.7 - - + +
330I LEU* 1.3 60.0 + - - +
332I ARG* 2.9 32.0 + - - +
333I ASN* 2.9 50.4 + - - +
375I LEU* 5.0 3.0 - - - +
376I TYR* 2.9 35.4 + - + -
423I TYR* 3.6 47.6 - - + +
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Residues in contact with LEU 330 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326I THR* 2.9 32.6 + - + +
327I LEU* 3.9 8.3 - - + +
329I GLU* 1.3 76.6 - - - +
331I ALA* 1.3 61.1 + - - +
333I ASN 3.3 21.1 - - - +
334I PRO* 3.6 0.5 - - - +
336I VAL* 4.6 7.6 - - + -
337I GLN* 2.8 31.1 - - + +
340I LEU* 3.5 31.0 - - + -
365I LEU* 5.1 1.1 - - + -
423I TYR* 4.1 23.1 - - + +
464I LEU* 4.6 12.6 - - + -
468I LEU* 4.1 29.6 - - + -
473I VAL* 5.4 4.5 - - + -
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Residues in contact with ALA 331 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280H PHE* 5.7 3.5 - - - -
327I LEU 3.1 17.0 + - - +
328I PHE 3.2 3.8 + - - +
330I LEU* 1.3 75.6 - - - +
332I ARG* 1.3 62.7 + - - +
333I ASN 3.2 0.6 + - - -
334I PRO* 3.7 11.4 - - - +
337I GLN* 4.0 0.2 + - - -
473I VAL* 3.5 28.8 - - + +
474I GLU* 3.9 13.1 - - - +
475I THR* 3.6 25.9 + - - +
478I GLN* 4.4 5.5 + - - +
497I LEU* 4.2 7.2 - - + -
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Residues in contact with ARG 332 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328I PHE* 3.0 56.0 + - + +
329I GLU* 2.9 38.3 + - - +
331I ALA* 1.3 75.7 - - - +
333I ASN* 1.3 66.1 + - - +
334I PRO* 3.4 8.4 - - - +
376I TYR* 4.0 4.6 + - - -
475I THR* 4.8 1.1 - - - +
477I THR 4.6 0.4 - - - +
478I GLN* 2.8 58.8 + - + +
480I ASP* 3.4 40.2 + - - +
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Residues in contact with ASN 333 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329I GLU* 2.9 37.8 + - - +
330I LEU* 3.3 6.6 - - - +
331I ALA 3.2 1.2 - - - -
332I ARG* 1.3 83.1 + - - +
334I PRO* 1.3 68.3 - - - +
335I ASP* 3.1 10.2 + - - +
336I VAL* 3.0 28.6 + - + +
337I GLN 3.1 8.8 + - - -
422I ARG* 6.0 2.8 - - - +
423I TYR* 3.6 30.0 + - + +
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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
------------------------------------------------------------
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