Contacts of the helix formed by residues 387 - 400 (chain B) in PDB entry 4YVF
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 PRO 387 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B ILE* 5.1 1.8 - - + -
371B GLU* 4.3 4.3 - - + +
378B LYS* 5.7 2.7 - - - +
379B TYR* 3.7 24.5 - - + +
385B PHE 3.1 9.2 - - - +
386B LEU* 1.3 90.7 - - + +
388B LYS* 1.3 66.5 + - - +
389B LYS* 4.5 6.3 - - + +
390B LEU* 2.9 43.1 + - + +
391B ASP* 3.3 8.1 + - - +
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Residues in contact with LYS 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ILE* 5.1 2.0 - - + +
431A ARG* 5.3 4.0 - - - +
184B VAL* 4.9 4.6 - - - +
386B LEU 3.3 4.4 + - - -
387B PRO* 1.3 71.8 - - - +
389B LYS* 1.3 63.1 + - - +
391B ASP* 3.1 11.2 + - + +
392B GLU* 3.0 43.1 + - + +
424B PRO* 4.0 14.8 - - + -
426B LYS* 3.0 25.1 - - + +
427B PRO 3.3 28.8 + - - -
428B ASP* 4.1 20.3 + - - +
430B TYR 5.1 0.6 + - - -
432B TYR* 2.8 38.3 + - - +
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Residues in contact with LYS 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B PRO* 3.2 5.4 - - + +
388B LYS* 1.3 77.9 - - - +
390B LEU* 1.3 67.5 + - + +
392B GLU* 3.6 14.8 + - - +
393B ALA* 3.2 22.9 + - - +
420B SER* 4.9 3.6 + - - -
422B ASP* 3.5 36.6 + - - +
423B GLY 3.5 20.7 + - - +
424B PRO* 4.2 17.4 - - + +
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Residues in contact with LEU 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B MET* 4.2 24.8 - - + +
371B GLU* 3.0 41.5 - - + +
386B LEU* 3.8 20.0 - - + -
387B PRO* 2.9 29.8 + - + +
389B LYS* 1.3 84.8 - - + +
391B ASP* 1.3 59.1 + - - +
392B GLU 3.1 1.8 - - - -
393B ALA* 3.0 9.5 + - + +
394B VAL* 2.8 32.9 + - - +
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Residues in contact with ASP 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ILE* 4.1 10.7 - - + +
431A ARG* 5.1 0.5 + - - -
183B SER* 3.5 9.7 - - - -
184B VAL* 2.7 39.1 + - - +
185B THR* 2.5 43.4 + - - +
386B LEU* 4.0 14.5 - - + +
387B PRO 3.3 6.0 + - - +
388B LYS* 3.1 18.0 + - + +
390B LEU* 1.3 77.8 - - - +
392B GLU* 1.3 61.3 + - - +
394B VAL* 3.2 4.5 + - - +
395B ALA 3.2 16.3 + - - -
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Residues in contact with GLU 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A ASP* 3.9 6.8 - - - +
246A PRO* 3.2 22.9 - - + +
247A ILE* 3.6 24.5 - - + -
388B LYS* 3.0 26.3 + - + +
389B LYS* 3.7 13.3 - - - +
391B ASP* 1.3 76.0 - - - +
393B ALA* 1.3 53.2 + - - +
395B ALA* 3.2 0.9 + - - +
396B GLU* 2.7 33.1 + - - +
422B ASP 4.2 3.1 - - - +
423B GLY* 3.9 4.5 - - - -
424B PRO* 3.4 19.9 - - - +
425B PHE* 3.0 44.5 + - + +
426B LYS 4.1 0.3 + - - -
432B TYR* 4.8 1.0 + - - -
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Residues in contact with ALA 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ARG* 5.2 9.9 - - - +
367B MET* 3.7 19.0 - - + +
389B LYS 3.2 14.9 + - - +
390B LEU* 3.0 16.7 + - + +
392B GLU* 1.3 74.7 - - - +
394B VAL* 1.3 65.3 + - - +
396B GLU* 3.8 10.1 - - - +
397B ALA* 2.9 25.1 + - - +
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Residues in contact with VAL 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B THR* 3.6 20.0 - - - +
360B ASN* 3.7 19.5 - - - +
363B THR* 3.9 14.4 - - + -
364B ASN* 3.8 24.0 - - - +
367B MET* 3.7 23.1 - - + -
386B LEU* 4.8 0.2 - - + -
390B LEU 2.8 19.5 + - - +
391B ASP* 3.4 9.4 - - - +
392B GLU 3.2 0.2 - - - -
393B ALA* 1.3 79.3 - - - +
395B ALA* 1.3 55.8 + - - +
397B ALA* 3.3 4.7 + - - +
398B HIS* 2.6 44.9 + - + -
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Residues in contact with ALA 395 (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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246A PRO 3.6 24.9 - - - +
247A ILE* 3.8 10.1 - - + +
250A LEU* 3.7 18.4 - - + +
185B THR* 3.6 20.1 - - + +
391B ASP 3.2 2.0 + - - -
392B GLU 3.5 7.6 - - - +
394B VAL* 1.3 78.4 - - - +
396B GLU* 1.3 64.5 + - - +
398B HIS* 3.0 14.3 + - - +
399B LEU* 3.3 17.0 + - - +
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Residues in contact with GLU 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A PRO* 3.6 17.2 - - + +
392B GLU* 2.7 20.3 + - - +
393B ALA* 3.8 9.7 - - - +
395B ALA* 1.3 72.3 - - - +
397B ALA* 1.3 62.7 - - - +
399B LEU* 3.0 33.4 + - + +
400B GLY 4.0 3.1 + - - -
406B LEU* 4.2 18.0 - - + +
408B LYS* 5.8 1.9 + - - -
425B PHE* 5.8 2.3 - - - -
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Residues in contact with ALA 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B PRO* 3.8 20.3 - - - +
31B GLY* 3.7 20.6 - - - +
34B ARG* 3.8 30.4 - - + +
35B MET* 5.5 1.6 - - - -
363B THR* 4.8 3.1 - - + -
367B MET* 5.5 2.9 - - + -
393B ALA 2.9 17.5 + - - +
394B VAL* 3.4 9.4 - - - +
395B ALA 3.2 0.2 - - - -
396B GLU* 1.3 76.3 - - - +
398B HIS* 1.3 60.1 + - - +
400B GLY* 4.5 4.3 + - - -
401B LYS 5.2 0.2 + - - -
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Residues in contact with HIS 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A LEU* 4.5 9.4 - - + -
30B PRO* 3.7 20.0 - - + -
31B GLY* 3.4 16.5 - - - -
356B PHE* 3.9 19.8 - + + -
359B SER* 2.8 31.6 + - - -
360B ASN* 3.6 34.6 + - - -
363B THR* 3.8 9.9 - - - -
394B VAL* 2.6 33.0 + - + -
395B ALA 3.0 8.5 + - - +
397B ALA* 1.3 76.0 - - - +
399B LEU* 1.3 64.4 + - - +
400B GLY 3.3 2.8 + - - -
401B LYS* 3.7 6.1 + - - +
402B LEU* 3.4 23.9 + - - +
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Residues in contact with LEU 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A PRO* 3.7 43.5 - - + +
249A ALA* 4.3 2.2 - - + -
250A LEU* 4.0 26.5 - - + +
395B ALA 3.3 14.8 - - - +
396B GLU* 3.0 15.5 + - + +
398B HIS* 1.3 77.0 - - - +
400B GLY* 1.3 63.6 + - - +
402B LEU* 3.4 3.2 + - + -
403B ASN 2.9 3.6 + - - -
404B VAL* 2.9 58.1 + - + +
406B LEU* 4.0 25.1 - - + -
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Residues in contact with GLY 400 (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 GLU 4.0 4.2 + - - -
397B ALA 4.5 3.1 + - - -
398B HIS* 3.3 1.0 - - - +
399B LEU* 1.3 79.0 - - - +
401B LYS* 1.3 57.0 + - - +
403B ASN* 2.8 24.3 + - - +
404B VAL 5.0 2.7 - - - -
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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