Contacts of the helix formed by residues 445 - 454 (chain A) in PDB entry 4FWF
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 445 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269A PHE* 5.5 0.9 - - - -
439A VAL* 3.4 19.5 - - + +
440A ASN 4.4 4.9 + - - +
441A GLY 2.8 28.9 + - - +
442A CYS* 3.1 11.8 + - - +
443A ILE 3.0 3.6 + - - -
444A ASN* 1.3 78.0 - - - +
446A PRO* 1.3 79.1 - - - +
447A VAL* 3.1 10.6 + - - +
448A ALA* 2.9 23.8 + - - +
449A LEU* 3.2 9.7 + - - +
568A PHE* 3.4 11.6 - - + -
806A THR* 2.8 34.9 + - - +
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Residues in contact with PRO 446 (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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282A LEU* 4.4 5.4 - - + -
444A ASN 3.4 7.4 - - - +
445A ASN* 1.3 91.4 - - - +
447A VAL* 1.3 63.0 + - + +
449A LEU* 3.3 14.8 + - + +
450A MET* 3.0 29.1 + - + +
568A PHE* 4.1 6.7 - - + -
806A THR* 3.8 21.3 - - + +
809A TYR* 3.6 38.6 - - + -
810A LEU* 4.0 12.8 - - + -
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Residues in contact with VAL 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A VAL* 3.7 29.2 - - + -
445A ASN* 3.1 12.4 + - - +
446A PRO* 1.3 77.8 - - + +
448A ALA* 1.3 63.3 + - - +
450A MET* 3.1 18.9 + - + +
451A CYS* 3.0 27.8 + - - -
458A MET* 4.9 1.3 - - - -
575A LEU* 4.3 4.0 - - + -
579A TYR* 3.8 27.4 - - + +
582A ILE* 4.2 11.4 - - + -
805A VAL* 4.6 8.1 - - + -
806A THR* 3.7 22.0 - - - +
809A TYR* 5.9 0.9 - - + -
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Residues in contact with ALA 448 (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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266A ASN* 5.2 2.4 + - - -
268A TYR* 4.1 16.9 - - + +
269A PHE* 4.5 4.8 - - + -
439A VAL* 5.4 0.2 - - - +
442A CYS* 3.3 26.9 - - + +
444A ASN 5.4 0.2 - - - +
445A ASN* 2.9 14.5 + - + +
447A VAL* 1.3 78.5 - - - +
449A LEU* 1.3 60.6 + - - +
451A CYS* 3.4 3.8 + - - +
452A GLU* 3.1 21.3 + - - +
458A MET* 4.0 23.9 - - + +
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Residues in contact with LEU 449 (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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269A PHE* 3.7 25.2 - - + -
318A TRP* 3.9 23.6 - - + +
319A TYR* 4.5 7.4 - - + -
322A CYS* 3.7 37.5 - - + -
364A THR* 4.4 4.3 - - - +
365A GLY* 3.8 31.6 - - - +
445A ASN 3.2 7.4 + - - +
446A PRO* 3.6 16.2 - - + +
447A VAL 3.3 0.2 - - - -
448A ALA* 1.3 79.1 - - - +
450A MET* 1.3 56.5 + - - +
452A GLU* 3.3 2.8 + - - +
453A GLN* 3.0 34.5 + - - +
809A TYR* 5.7 0.2 - - - +
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Residues in contact with MET 450 (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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365A GLY* 3.7 24.9 - - - -
366A VAL* 3.8 16.2 - - + +
446A PRO 3.0 32.1 + - - +
447A VAL* 3.1 19.2 + - + +
449A LEU* 1.3 75.4 - - - +
451A CYS* 1.3 58.9 + - - +
453A GLN* 3.2 11.0 + - - +
454A LEU* 3.0 35.2 + - - +
582A ILE* 3.7 37.0 - - + -
586A LEU* 4.6 2.5 - - + -
805A VAL* 6.4 0.4 - - + -
809A TYR* 3.9 40.2 - - + -
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Residues in contact with CYS 451 (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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447A VAL* 3.0 18.4 + - - +
448A ALA 3.6 8.1 - - - +
450A MET* 1.3 78.0 - - - +
452A GLU* 1.3 55.2 + - - +
455A GLY* 3.0 7.6 + - - -
456A ILE* 2.8 62.0 + - + +
458A MET* 3.9 21.5 - - + -
575A LEU* 3.5 31.6 - - - -
582A ILE* 4.2 8.5 - - - -
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Residues in contact with GLU 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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266A ASN* 2.7 38.7 + - - +
269A PHE* 3.9 16.3 - - + -
322A CYS* 3.9 20.6 - - - -
323A LYS* 4.4 17.6 + - + +
448A ALA 3.1 13.7 + - - +
449A LEU 3.5 8.1 - - - +
450A MET 3.2 0.2 - - - -
451A CYS* 1.3 76.1 - - - +
453A GLN* 1.3 64.8 + - - +
455A GLY* 3.2 12.6 + - - -
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Residues in contact with GLN 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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318A TRP* 3.8 6.9 - - - -
322A CYS* 3.0 36.7 + - - +
323A LYS* 3.4 28.3 - - + +
364A THR 3.0 24.7 + - - -
365A GLY* 3.4 4.0 - - - -
366A VAL* 2.8 37.4 + - + +
367A LEU* 3.8 8.9 - - - +
449A LEU* 3.0 23.9 + - - +
450A MET* 3.2 13.1 + - - +
452A GLU* 1.3 77.4 - - - +
454A LEU* 1.3 60.5 + - - +
455A GLY 3.3 0.9 + - - -
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Residues in contact with LEU 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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366A VAL* 3.7 17.3 - - + -
450A MET 3.0 19.0 + - - +
451A CYS 4.4 0.7 - - - +
453A GLN* 1.3 75.9 - - - +
455A GLY* 1.3 64.5 + - - +
456A ILE* 3.2 27.1 + - + +
581A VAL* 4.4 6.1 - - + +
582A ILE* 4.2 35.4 - - + +
585A LYS* 3.6 38.8 - - + -
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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