Contacts of the helix formed by residues 451 - 459 (chain A) in PDB entry 3F7D
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 451 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267A CAF 3.9 23.3 + - - +
268A ARG* 4.7 8.3 - - - +
271A ASP* 3.4 26.0 + - - +
446A GLU* 2.9 21.1 + - - +
449A ARG* 5.3 0.5 - - - +
450A ASN* 1.3 78.8 - - + +
452A LEU* 1.3 63.0 + - - +
453A LEU* 3.0 21.5 + - - +
454A ILE* 3.1 32.3 + - + +
455A GLU* 3.4 7.8 + - - +
141B LEU* 3.6 8.1 - - - +
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Residues in contact with LEU 452 (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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271A ASP* 3.1 16.0 + - - +
274A PHE* 3.4 35.2 - - + -
275A ILE* 4.3 14.4 - - + -
278A VAL* 4.1 6.5 - - + -
450A ASN 3.9 1.6 + - - -
451A ASN* 1.3 71.6 - - - +
453A LEU* 1.3 60.0 + - - +
455A GLU* 3.0 10.9 + - - +
456A MET* 2.9 29.1 + - + +
141B LEU* 3.7 18.6 - - + +
142B LEU* 3.4 41.7 - - + +
145B LEU* 3.4 26.2 - - + -
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Residues in contact with LEU 453 (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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1A P42 5.7 3.4 - - + -
267A CAF 3.3 28.5 - - + +
270A ALA* 3.7 30.5 - - + +
271A ASP* 3.1 13.9 + - - +
274A PHE* 3.5 31.6 - - + -
303A TRP* 3.5 33.6 - - + -
307A LEU* 3.8 14.8 - - + -
438A LEU* 5.9 2.0 - - + -
451A ASN* 3.0 6.0 + - - +
452A LEU* 1.3 75.0 - - - +
454A ILE* 1.3 62.5 + - - +
456A MET* 3.1 5.3 + - + +
457A LEU* 2.8 31.1 + - - +
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Residues in contact with ILE 454 (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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267A CAF 3.2 34.3 - - + -
443A LEU* 3.5 22.0 - - + -
444A GLY 4.1 13.0 - - - +
445A ASN* 5.0 3.1 - - - +
446A GLU* 3.9 13.0 - - + +
451A ASN* 3.1 33.6 + - + +
452A LEU 3.3 0.2 - - - -
453A LEU* 1.3 74.8 - - - +
455A GLU* 1.3 65.0 + - - +
457A LEU* 3.2 7.9 + - + +
458A GLN* 3.1 49.7 + - + +
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Residues in contact with GLU 455 (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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296A MET* 4.9 1.6 - - - +
300A GLN* 6.0 0.2 - - - +
445A ASN* 6.2 0.2 - - - +
449A ARG* 3.4 39.7 + - - +
451A ASN 3.4 5.6 + - - +
452A LEU* 3.0 14.2 + - - +
454A ILE* 1.3 79.1 - - - +
456A MET* 1.3 67.0 + - - +
458A GLN* 3.3 7.5 + - - +
459A ALA* 2.9 26.8 + - + +
139B PRO 3.5 0.9 - - - +
140B SER* 3.5 8.1 + - - -
141B LEU* 3.0 28.7 + - + +
142B LEU* 3.0 36.5 + - - +
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Residues in contact with MET 456 (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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274A PHE* 3.8 27.6 - - + -
299A LEU 3.3 29.4 - - - +
300A GLN* 2.8 48.1 + - - +
303A TRP* 3.6 33.3 + - + -
452A LEU* 2.9 20.9 + - - +
453A LEU* 3.1 13.2 + - + +
455A GLU* 1.3 78.5 - - - +
457A LEU* 1.3 62.2 + - - +
459A ALA 3.4 3.8 + - - +
142B LEU* 3.7 30.7 - - + -
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Residues in contact with LEU 457 (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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267A CAF 5.0 2.5 - - + -
303A TRP* 3.9 24.0 - - + -
435A LYS* 3.9 14.1 - - + -
438A LEU* 3.5 40.4 - - + +
439A TYR* 3.4 60.0 + - + +
443A LEU* 4.5 15.3 - - + -
453A LEU 2.8 15.7 + - - +
454A ILE* 3.6 7.4 - - + +
455A GLU 3.2 0.2 - - - -
456A MET* 1.3 79.0 - - - +
458A GLN* 1.3 64.0 + - + +
459A ALA 3.3 4.5 + - - +
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Residues in contact with GLN 458 (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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439A TYR* 5.6 1.3 - - + -
443A LEU* 3.7 23.0 + - - +
445A ASN* 3.0 39.8 + - - +
449A ARG* 5.3 2.3 + - - -
454A ILE* 3.1 33.6 + - + +
455A GLU* 3.7 5.1 - - - +
457A LEU* 1.3 79.3 - - + +
459A ALA* 1.3 65.1 + - - +
460A LYS* 3.6 4.2 + - - +
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Residues in contact with ALA 459 (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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300A GLN* 3.2 44.0 + - + +
455A GLU* 2.9 18.1 + - + +
456A MET 4.2 0.2 - - - +
457A LEU 3.3 6.6 - - - +
458A GLN* 1.3 80.6 - - - +
460A LYS* 1.3 62.2 + - - +
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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