Contacts of the helix formed by residues 411 - 429 (chain B) in PDB entry 3MDL
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 ASN 411 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275B TYR* 3.7 21.0 + - - -
279B ILE* 5.9 0.6 - - - +
283B LEU* 3.5 31.0 + - + +
285B PHE* 3.7 31.0 - - + -
293B GLY* 4.1 15.0 + - - +
296B PRO* 4.0 13.0 - - - +
299B MET* 3.5 22.7 - - - +
409B TYR 3.7 4.6 + - - -
410B ASN* 1.3 69.0 - - - +
412B SER* 1.3 64.3 - - - +
413B ILE 3.1 2.0 - - - -
414B LEU* 3.1 19.2 + - + +
415B LEU* 3.2 15.2 + - - +
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Residues in contact with SER 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B LEU* 3.2 34.6 - - - +
410B ASN* 3.2 15.4 + - - -
411B ASN* 1.3 76.6 - - - +
413B ILE* 1.3 54.0 + - - +
415B LEU* 3.2 4.8 + - - +
416B GLU* 2.8 37.6 + - - +
681B NAG 3.9 15.7 - - - -
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Residues in contact with ILE 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B PRO* 4.8 1.1 - - + -
397B ILE* 4.6 2.2 - - + -
402B TYR* 3.7 34.3 - - + -
406B GLN 3.6 24.7 - - - +
407B PHE* 4.0 18.2 - - + -
410B ASN* 3.5 19.7 - - + +
411B ASN 3.1 0.6 - - - -
412B SER* 1.3 76.2 - - - +
414B LEU* 1.3 61.8 + - - +
416B GLU* 4.3 2.2 - - - -
417B HIS* 3.1 47.0 + - + -
422B PHE* 3.6 20.4 - - + -
681B NAG 3.4 28.0 - - - +
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Residues in contact with LEU 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B TYR* 3.9 15.3 + - + -
285B PHE* 5.2 3.8 - - + -
296B PRO* 4.4 4.9 - - + +
299B MET* 3.9 44.2 - - + +
300B MET* 3.9 7.2 - - + +
303B THR* 4.2 7.9 - - - +
410B ASN 4.4 0.6 + - - -
411B ASN* 3.1 14.9 + - - +
413B ILE* 1.3 78.9 - - - +
415B LEU* 1.3 54.8 + - + +
418B GLY* 2.7 35.2 + - - -
419B LEU* 3.8 24.0 - - + +
422B PHE* 3.6 42.5 - - + -
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Residues in contact with LEU 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B ILE* 4.0 23.3 - - + -
262B TYR* 3.6 43.2 + - + -
282B ASN* 5.5 4.3 - - - +
283B LEU* 3.6 29.6 - - + -
285B PHE* 3.9 22.0 - - + -
411B ASN 3.2 10.5 + - - +
412B SER* 3.8 6.3 - - - +
414B LEU* 1.3 77.6 - - + +
416B GLU* 1.3 63.0 + - - +
418B GLY* 3.9 5.9 + - - -
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Residues in contact with GLU 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B TYR* 5.0 1.6 - - - +
412B SER 2.8 21.2 + - - +
413B ILE 3.8 2.5 - - - +
415B LEU* 1.3 75.2 - - - +
417B HIS* 1.3 81.9 + - + +
681B NAG 4.1 17.6 - - - +
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Residues in contact with HIS 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397B ILE* 3.5 41.7 - - + +
398B GLU* 3.0 27.4 + - + +
400B GLN* 3.9 12.1 - - + -
402B TYR* 2.8 27.4 + - - -
413B ILE* 3.1 38.8 + - + +
415B LEU 4.4 0.4 - - - -
416B GLU* 1.3 93.3 - - + +
418B GLY* 1.3 67.6 + - - +
421B GLN* 3.6 20.2 + - + +
422B PHE* 4.1 3.1 - - + -
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Residues in contact with GLY 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B GLU* 6.1 1.6 - - - -
262B TYR* 4.0 9.9 - - - -
414B LEU 2.7 24.5 + - - -
415B LEU 3.9 3.5 + - - -
416B GLU 3.6 1.2 - - - -
417B HIS* 1.3 77.2 - - - +
419B LEU* 1.3 64.9 + - - -
420B THR* 3.3 2.9 + - - -
421B GLN 3.4 0.3 + - - -
422B PHE* 3.1 23.5 + - - -
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Residues in contact with LEU 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B GLU* 5.3 6.0 + - - +
262B TYR* 3.6 33.3 + - + +
300B MET* 4.0 15.0 - - + +
303B THR* 4.0 23.8 - - + -
304B ILE* 3.6 31.9 - - + +
307B ARG* 4.0 22.4 - - - +
414B LEU* 3.8 15.3 - - + -
418B GLY* 1.3 68.5 - - - -
420B THR* 1.3 59.6 + - - +
422B PHE* 3.2 6.7 + - - +
423B VAL* 2.8 34.2 + - + +
572B VAL* 3.9 13.9 - - + -
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Residues in contact with THR 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B GLU* 5.7 0.2 + - - -
418B GLY* 3.3 1.0 - - - -
419B LEU* 1.3 78.1 - - - +
421B GLN* 1.3 58.9 + - + +
423B VAL* 3.3 2.8 + - - +
424B GLU* 2.9 48.2 + - - +
572B VAL* 3.6 12.0 - - - +
573B LYS* 2.7 40.9 + - - +
574B GLY* 5.3 2.2 - - - -
576B PRO* 4.2 10.4 - - + +
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Residues in contact with GLN 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397B ILE* 4.6 2.7 - - + -
398B GLU* 3.4 42.2 - - - +
417B HIS* 3.6 29.1 + - + +
418B GLY 3.4 3.0 + - - +
419B LEU 3.3 0.2 - - - -
420B THR* 1.3 76.0 - - + +
422B PHE* 1.3 61.8 + - - +
424B GLU* 3.0 27.2 + - - +
425B SER* 2.8 51.7 + - - -
428B ARG* 4.7 4.8 + - - +
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Residues in contact with PHE 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B PRO* 3.7 30.5 - - + -
300B MET* 3.9 19.5 - - + -
397B ILE* 4.0 25.8 - - + -
407B PHE* 4.7 1.3 - + - -
413B ILE* 3.6 43.3 - - + -
414B LEU* 3.6 26.7 - - + -
417B HIS* 4.1 2.2 - - + -
418B GLY 3.1 19.3 + - - +
419B LEU* 3.2 11.6 + - - +
421B GLN* 1.3 75.5 - - - +
423B VAL* 1.3 56.7 + - - +
425B SER* 4.7 0.7 - - - -
426B PHE* 2.8 67.7 + + - +
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Residues in contact with VAL 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B MET* 4.1 15.7 - - + -
300B MET* 4.4 9.0 - - + -
304B ILE* 4.5 2.9 - - + -
419B LEU* 2.8 23.6 + - - +
420B THR 3.7 3.8 - - - +
422B PHE* 1.3 72.3 - - - +
424B GLU* 1.3 61.1 + - - +
426B PHE* 4.2 0.2 - - - +
427B THR* 2.6 42.3 + - - +
568B ILE* 3.9 21.5 - - + -
572B VAL* 4.2 15.7 - - + -
576B PRO* 3.8 19.5 - - + -
577B PHE 4.1 3.6 - - - +
578B THR* 3.9 20.9 - - - +
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Residues in contact with GLU 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420B THR* 2.9 35.2 + - - +
421B GLN* 3.0 30.0 + - - +
423B VAL* 1.3 77.9 - - - +
425B SER* 1.3 60.8 + - - +
427B THR* 3.6 4.8 + - - -
428B ARG* 3.4 37.6 + - - +
576B PRO* 3.9 19.2 - - + +
577B PHE 5.4 3.4 - - - +
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Residues in contact with SER 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396B ASN 3.3 21.7 - - - +
397B ILE* 3.5 11.9 - - - +
398B GLU 2.9 23.9 + - - -
421B GLN* 2.8 32.4 + - - -
422B PHE 3.9 1.6 - - - -
424B GLU* 1.3 71.0 - - - +
426B PHE* 1.3 65.5 + - - +
428B ARG* 3.1 20.2 + - - +
429B GLN* 3.1 23.7 + - - +
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Residues in contact with PHE 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B ASN* 3.4 1.9 - - - +
196B MET* 3.1 52.2 + - + +
197B MET* 3.4 18.6 + - - +
200B PHE* 3.4 36.3 - + - -
297B GLY* 4.1 6.1 - - - -
300B MET* 3.9 17.0 - - + -
395B PHE* 4.7 6.3 - + + -
396B ASN 4.8 0.2 - - - -
397B ILE* 3.2 30.7 - - + -
407B PHE* 3.8 15.7 - + - -
422B PHE* 2.8 44.6 + + - +
425B SER* 1.3 73.6 - - - +
427B THR* 1.3 63.9 + - - +
428B ARG 3.5 0.2 + - - -
429B GLN* 3.6 12.9 + - - +
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Residues in contact with THR 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B ASN* 3.1 29.1 + - - +
197B MET* 3.3 4.0 - - - +
423B VAL* 2.6 25.7 + - - +
424B GLU* 3.8 5.6 - - - -
426B PHE* 1.3 76.5 - - - +
428B ARG* 1.3 58.4 + - + +
577B PHE 3.9 6.7 + - - +
578B THR* 3.0 39.0 + - - -
579B SER* 4.1 5.2 - - - +
581B ASN 4.0 5.5 - - - +
582B VAL* 3.2 19.9 - - + +
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Residues in contact with ARG 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396B ASN* 4.6 6.3 + - - +
398B GLU* 4.0 20.6 + - - +
421B GLN* 4.7 4.4 + - - +
424B GLU* 3.4 30.0 + - - +
425B SER* 3.1 34.0 + - - +
427B THR* 1.3 78.8 - - + +
429B GLN* 1.3 62.5 + - + +
430B ILE* 3.5 1.6 + - - +
582B VAL* 3.3 19.3 - - + +
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Residues in contact with GLN 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B ASN* 3.2 4.3 - - - -
196B MET* 3.1 47.9 + - + +
392B PRO* 3.2 17.5 - - - +
394B THR* 2.8 26.6 + - - -
395B PHE* 3.8 2.8 - - - -
396B ASN* 2.8 51.4 + - + +
425B SER 3.1 14.0 + - - +
426B PHE* 3.6 4.2 + - - -
427B THR 3.5 1.0 - - - -
428B ARG* 1.3 76.3 - - - +
430B ILE* 1.3 69.0 + - + +
582B VAL 4.1 1.3 - - - -
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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