Contacts of the helix formed by residues 408 - 420 (chain A) in PDB entry 3VF1
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 GLY 408 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A VAL* 5.2 8.0 + - - +
175A GLN 5.7 3.1 - - - -
176A PHE* 4.9 2.1 - - - -
406A THR 3.3 1.8 + - - -
407A LYS* 1.3 75.9 - - - +
409A ILE* 1.3 63.0 + - - +
410A MET 3.3 3.1 - - - +
411A ALA* 3.5 12.8 + - - +
412A ILE* 3.2 24.4 + - - +
677A ILE 3.6 5.1 - - - +
678A ALA* 4.2 10.2 - - - -
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Residues in contact with ILE 409 (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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378A HIS 3.4 25.8 - - - +
381A MET* 3.5 26.5 - - + +
382A GLU* 3.5 11.9 - - - +
385A ALA* 3.6 24.0 - - + -
406A THR* 3.3 23.8 - - - +
407A LYS 3.3 1.8 - - - -
408A GLY* 1.3 78.7 - - - +
410A MET* 1.3 67.0 + - + +
412A ILE* 3.2 2.3 - - - +
413A ASN* 3.1 32.0 + - - +
552A CYS* 5.1 4.9 - - - -
677A ILE* 3.3 34.4 + - + +
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Residues in contact with MET 410 (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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146A TYR* 4.1 11.4 - - + -
162A VAL* 4.0 37.7 - - + -
170A LEU* 4.0 9.6 - - + -
174A VAL* 3.6 26.0 - - + -
382A GLU* 4.3 19.1 - - + -
385A ALA* 4.4 17.0 - - + -
386A VAL* 4.1 10.3 - - + -
389A TRP* 3.4 35.2 - - + +
406A THR 4.9 2.0 + - - +
408A GLY* 3.3 0.6 - - - -
409A ILE* 1.3 81.6 - - + +
411A ALA* 1.3 63.7 + - - +
413A ASN* 3.5 1.2 + - - +
414A THR* 2.8 31.6 + - - -
417A ARG* 4.5 0.3 + - - -
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Residues in contact with ALA 411 (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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167A PRO* 4.4 4.1 - - + +
170A LEU* 3.8 13.3 - - + +
174A VAL 3.5 19.3 + - - +
175A GLN* 4.1 2.2 - - - -
176A PHE* 3.4 44.3 - - + +
408A GLY* 3.5 11.1 + - - +
409A ILE 3.4 0.8 - - - -
410A MET* 1.3 80.9 - - - +
412A ILE* 1.3 64.3 + - - +
414A THR* 3.3 3.3 + - - -
415A LEU* 3.2 16.8 + - - +
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Residues in contact with ILE 412 (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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176A PHE* 3.5 14.8 - - + -
181A THR* 5.0 1.1 - - + -
185A PHE* 3.7 33.9 - - + -
378A HIS* 4.0 19.2 + - + +
408A GLY 3.2 12.8 + - - +
409A ILE* 3.2 13.0 - - - +
411A ALA* 1.3 79.2 - - - +
413A ASN* 1.3 70.3 + - - +
415A LEU* 3.3 10.1 + - + +
416A GLY* 2.8 24.4 + - - -
420A LEU* 5.2 3.0 - - + +
677A ILE* 3.8 15.3 - - + +
678A ALA 4.3 6.7 - - - +
679A ILE* 4.0 25.4 - - + +
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Residues in contact with ASN 413 (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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378A HIS* 2.9 60.5 + - - +
379A LEU* 3.8 9.9 - - + +
382A GLU* 2.8 36.6 + - - +
409A ILE* 3.1 18.1 + - - +
410A MET 4.1 0.9 - - - +
412A ILE* 1.3 80.2 - - - +
414A THR* 1.3 60.8 + - - +
416A GLY* 3.6 3.0 - - - +
417A ARG* 2.9 41.9 + - - +
421A ILE* 5.6 0.7 - - - +
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Residues in contact with THR 414 (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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162A VAL* 4.0 7.4 - - - +
164A ALA* 3.8 20.1 - - + +
165A GLU 4.3 1.3 - - - -
166A GLU* 3.4 39.5 - - - +
167A PRO* 3.6 2.5 - - + -
170A LEU* 3.8 12.9 - - - +
410A MET 2.8 22.2 + - - -
411A ALA 3.6 4.5 - - - -
413A ASN* 1.3 76.4 - - - +
415A LEU* 1.3 61.7 + - - +
417A ARG* 3.4 27.9 + - - +
418A ASN* 3.4 16.7 + - - +
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Residues in contact with LEU 415 (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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167A PRO* 4.2 20.8 - - + +
176A PHE* 4.1 17.3 - - + -
181A THR* 3.8 21.1 - - + +
182A SER* 3.4 22.0 - - - +
184A LEU 5.4 0.4 - - - +
185A PHE* 3.7 33.0 - - + -
411A ALA 3.2 10.2 + - - +
412A ILE* 3.5 10.5 - - + +
413A ASN 3.2 0.2 - - - -
414A THR* 1.3 78.6 - - - +
416A GLY* 1.3 60.1 + - - +
418A ASN* 3.0 7.0 + - + +
419A ASP* 2.8 46.7 + - + +
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Residues in contact with GLY 416 (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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412A ILE 2.8 15.6 + - - -
413A ASN* 3.3 5.1 + - - -
415A LEU* 1.3 76.5 - - - +
417A ARG* 1.3 59.4 + - - +
420A LEU* 3.0 34.0 + - - +
421A ILE* 2.9 36.5 + - - +
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Residues in contact with ARG 417 (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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151A ASP* 5.0 2.5 - - - -
153A ARG* 3.3 16.0 + - - +
154A TYR* 2.7 62.9 + - + -
161A PHE* 3.3 32.6 - - - +
162A VAL* 3.9 9.9 + - - +
164A ALA 5.4 4.4 + - - -
379A LEU* 4.2 12.0 - - + +
382A GLU* 3.0 41.0 + - - -
410A MET 4.5 0.2 + - - -
413A ASN* 2.9 18.1 + - - +
414A THR* 3.6 36.7 + - - +
415A LEU 3.2 0.4 - - - -
416A GLY* 1.3 74.7 - - - +
418A ASN* 1.3 61.2 + - - +
421A ILE* 4.5 9.6 - - + -
422A PRO* 3.4 3.2 - - - +
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Residues in contact with ASN 418 (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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153A ARG* 3.0 27.6 + - - +
165A GLU 3.1 26.2 + - - +
166A GLU* 4.3 11.1 - - - +
167A PRO* 4.7 4.0 - - - +
414A THR* 3.4 15.7 + - - +
415A LEU* 3.0 7.8 + - + +
417A ARG* 1.3 80.3 - - - +
419A ASP* 1.3 71.6 + - - +
422A PRO* 3.1 21.1 - - - +
424A GLY 5.8 0.3 - - - -
425A GLY* 5.1 1.9 + - - -
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Residues in contact with ASP 419 (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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182A SER 4.5 5.2 - - - +
185A PHE* 4.3 23.3 + - + +
186A ARG* 5.3 6.8 + - - +
415A LEU* 2.8 38.0 + - + +
418A ASN* 1.3 90.3 - - - +
420A LEU* 1.3 65.1 + - - +
425A GLY* 3.3 8.9 - - - -
426A ALA* 3.0 20.1 + - - +
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Residues in contact with LEU 420 (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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185A PHE* 3.4 49.1 - - + -
374A LEU* 4.5 24.5 - - + -
378A HIS* 5.9 3.8 - - + +
412A ILE* 5.2 5.2 - - + +
416A GLY* 3.0 21.1 + - - +
419A ASP* 1.3 78.5 - - - +
421A ILE* 1.3 69.7 + - + +
422A PRO* 3.5 2.1 - - - +
425A GLY* 3.9 3.0 - - - -
426A ALA* 3.7 26.4 + - + +
427A ALA* 3.3 29.7 + - + +
609A VAL* 5.4 2.9 - - + -
613A LEU* 4.7 15.7 - - + -
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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