Contacts of the helix formed by residues 449 - 457 (chain X) in PDB entry 2W6C
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 449 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134X TYR* 4.1 11.3 - - - -
445X GLU 3.2 0.6 + - - -
446X PHE 2.9 9.0 + - - -
447X VAL 3.3 1.2 + - - -
448X PHE* 1.3 78.8 - - - +
450X LEU* 1.3 62.5 + - - +
451X PRO* 3.2 3.8 - - - -
452X LEU* 3.2 20.1 + - - +
453X VAL 4.6 0.3 + - - -
466X SER* 3.2 19.7 - - - -
470X MET* 3.6 16.4 - - - -
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Residues in contact with LEU 450 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128X ASP* 4.1 21.1 - - + +
129X VAL* 4.4 15.9 - - + +
131X ASN 5.4 1.1 - - - +
134X TYR* 4.2 20.2 - - + +
445X GLU* 3.0 24.2 + - + +
448X PHE* 3.6 25.6 - - + +
449X GLY* 1.3 73.2 - - - +
451X PRO* 1.3 69.3 - - + +
452X LEU 3.1 2.1 + - - -
453X VAL* 3.1 23.2 + - + +
456X LEU* 3.8 27.2 - - + +
458X TYR* 3.8 11.7 - - - +
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Residues in contact with PRO 451 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445X GLU 3.2 14.6 - - - +
446X PHE* 4.0 15.0 - - + -
449X GLY 3.2 5.2 - - - -
450X LEU* 1.3 91.6 - - + +
452X LEU* 1.3 60.6 + - - -
453X VAL 3.3 2.3 - - - +
454X LYS* 4.4 7.4 - - - +
458X TYR* 3.3 50.6 + - + +
462X GLU 3.9 14.8 - - - +
463X GLU* 3.5 18.7 - - - +
466X SER* 3.6 18.2 - - - +
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Residues in contact with LEU 452 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23X LEU* 3.4 41.2 - - + +
134X TYR* 5.4 4.5 - - + -
138X THR* 4.0 12.1 - - - +
449X GLY* 3.4 14.8 - - - +
450X LEU 3.1 1.4 + - - -
451X PRO* 1.3 80.3 - - - +
453X VAL* 1.3 64.2 + - + +
454X LYS* 3.5 14.3 + - - +
463X GLU* 4.0 30.5 - - + +
466X SER* 4.1 12.1 - - - +
467X ARG* 3.2 40.6 - - + +
470X MET* 4.1 12.8 - - + -
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Residues in contact with VAL 453 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23X LEU* 4.7 5.4 - - + -
134X TYR* 3.1 49.8 - - + +
450X LEU* 3.1 11.6 + - + +
451X PRO 4.5 3.3 - - - +
452X LEU* 1.3 78.0 - - - +
454X LYS* 1.3 64.1 + - - +
455X GLU* 4.0 13.9 - - + +
456X LEU* 3.0 48.7 + - + +
457X ASN 4.2 1.6 + - - -
458X TYR* 4.9 1.7 + - - -
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Residues in contact with LYS 454 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451X PRO 4.4 9.6 - - - +
452X LEU 3.5 11.1 + - - +
453X VAL* 1.3 67.4 - - - +
455X GLU* 1.3 62.4 + - - +
456X LEU 2.7 16.2 + - - -
457X ASN* 2.8 19.6 + - - +
458X TYR* 5.0 15.0 - - + +
459X THR 5.7 1.1 - - - -
460X ALA* 5.7 4.7 - - - +
463X GLU* 2.8 36.4 + - - -
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Residues in contact with GLU 455 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453X VAL* 3.7 14.9 - - + +
454X LYS* 1.3 84.0 + - - +
456X LEU* 1.3 66.0 + - + +
457X ASN* 3.6 7.0 - - - +
605X NAG 3.3 22.5 + - - +
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Residues in contact with LEU 456 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429X ASN* 3.2 14.7 + - - +
450X LEU* 3.8 37.9 - - + +
453X VAL* 3.0 32.4 + - + +
454X LYS 2.7 4.0 + - - -
455X GLU* 1.3 85.2 - - + +
457X ASN* 1.3 70.6 + - - +
458X TYR* 3.6 15.7 - - + +
605X NAG 4.5 22.2 - - + +
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Residues in contact with ASN 457 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428X SER* 4.3 4.7 + - - -
429X ASN* 3.7 19.1 + - + +
453X VAL 4.2 0.6 + - - -
454X LYS 2.8 15.0 + - - +
455X GLU* 3.6 4.7 - - - +
456X LEU* 1.3 81.4 - - - +
458X TYR* 1.3 64.4 + - - +
459X THR* 4.1 0.3 + - - +
605X NAG 1.5 59.1 + - - +
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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