Contacts of the helix formed by residues 443 - 461 (chain A) in PDB entry 3FR0
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 GLU 443 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ASP* 4.8 0.2 - - - +
85A ARG* 2.9 25.4 + - - -
87A MET* 3.3 32.0 - - - +
89A VAL* 5.7 0.2 - - + -
102A LYS* 3.9 21.5 + - + +
442A GLU* 1.3 85.2 + - - +
444A GLY* 1.3 64.7 + - - +
445A SER* 3.2 10.2 + - - -
446A GLY 3.2 18.8 + - - +
447A ARG* 3.0 40.0 + - + +
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Residues in contact with GLY 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A ALA 3.1 11.5 - - - +
209A THR* 4.3 4.7 - - - -
212A SER* 2.9 26.4 + - - -
409A ASP* 5.6 1.8 + - - -
441A SER* 3.7 19.7 + - - -
442A GLU 3.4 5.5 + - - -
443A GLU* 1.3 75.0 - - - +
445A SER* 1.3 56.3 + - - +
448A GLY* 2.9 25.1 + - - -
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Residues in contact with SER 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ASP* 3.0 39.3 + - - -
87A MET* 4.7 0.2 - - - -
149A THR* 3.0 34.5 + - - +
205A ASP* 4.7 5.9 - - - +
208A ALA* 3.6 8.2 - - - +
209A THR* 4.6 3.6 + - - -
409A ASP* 5.5 6.0 + - - -
443A GLU* 3.2 7.7 + - - -
444A GLY* 1.3 77.1 - - - +
446A GLY* 1.3 62.4 + - - +
449A ALA* 3.0 14.6 + - - +
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Residues in contact with GLY 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A SER* 2.8 27.0 + - - -
77A LEU 6.0 0.7 - - - -
87A MET* 3.5 30.3 - - - +
89A VAL* 3.9 6.1 - - - -
443A GLU* 3.2 8.2 + - - -
445A SER* 1.3 78.1 - - - +
447A ARG* 1.3 64.4 + - - +
449A ALA* 3.2 1.8 + - - -
450A ALA* 3.0 13.0 + - - +
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Residues in contact with ARG 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A VAL* 4.0 23.3 - - + -
100A SER* 2.9 43.6 + - - +
101A VAL* 3.9 12.1 - - - +
102A LYS 4.3 2.5 - - - +
212A SER* 3.9 32.0 + - - +
215A TYR* 5.8 2.4 - - - +
442A GLU* 3.3 36.4 - - - +
443A GLU* 3.0 35.9 + - + +
446A GLY* 1.3 76.3 - - - +
448A GLY* 1.3 58.1 + - - +
450A ALA* 3.7 0.3 - - - +
451A LEU* 2.9 38.4 + - + +
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Residues in contact with GLY 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A ALA* 3.3 22.4 - - - -
211A ILE* 3.9 2.1 - - - +
212A SER* 3.2 10.7 + - - -
444A GLY 2.9 23.6 + - - -
447A ARG* 1.3 78.3 - - - +
449A ALA* 1.3 61.8 + - - +
451A LEU* 3.4 2.8 + - - +
452A VAL* 3.2 28.8 + - - +
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Residues in contact with ALA 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A SER* 3.6 14.6 - - - +
147A GLY* 3.9 20.9 - - - +
148A PHE 4.2 0.7 - - - +
149A THR* 3.5 17.0 - - - +
201A ALA* 4.9 1.6 - - - +
203A VAL* 4.3 13.9 - - + -
208A ALA* 3.9 1.2 - - - +
445A SER 3.0 18.3 + - - +
448A GLY* 1.3 75.5 - - - +
450A ALA* 1.3 56.4 + - - +
452A VAL* 3.4 4.1 + - - +
453A SER* 3.0 31.9 + - - -
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Residues in contact with ALA 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A PHE* 4.1 18.4 - - + -
76A SER* 3.7 6.0 + - - +
89A VAL* 3.7 32.1 - - + -
91A VAL* 4.3 6.4 - - + +
147A GLY* 5.2 1.1 - - - -
446A GLY 3.0 16.7 + - - +
447A ARG 3.7 2.0 - - - +
448A GLY 3.2 0.2 - - - -
449A ALA* 1.3 75.1 - - - +
451A LEU* 1.3 59.4 + - - +
453A SER* 3.2 7.1 + - - -
454A ALA* 2.8 30.7 + - - +
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Residues in contact with LEU 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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91A VAL* 4.4 4.3 - - + -
98A GLN* 3.8 28.7 - - + +
99A TRP 4.3 0.2 - - - +
100A SER* 3.8 28.7 - - - +
211A ILE* 3.8 20.9 - - + +
212A SER* 4.0 14.4 - - - +
215A TYR* 3.4 39.1 + - + -
447A ARG* 2.9 28.6 + - + +
448A GLY 3.7 4.0 - - - +
450A ALA* 1.3 76.7 - - - +
452A VAL* 1.3 61.2 + - - +
454A ALA* 3.5 6.6 + - - +
455A VAL* 3.4 24.6 + - - +
501A AJB 4.1 3.4 + - - -
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Residues in contact with VAL 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A VAL* 4.3 6.1 - - + -
159A ILE* 4.1 8.7 - - + -
201A ALA* 4.1 16.4 - - + -
203A VAL* 4.1 23.1 - - + -
207A VAL* 5.2 0.4 - - + -
208A ALA* 5.7 0.2 - - - -
211A ILE* 3.6 29.8 - - + -
448A GLY 3.2 18.3 + - - +
449A ALA 3.8 4.0 - - - +
450A ALA 3.1 0.4 - - - -
451A LEU* 1.3 76.4 - - - +
453A SER* 1.3 59.9 + - - +
455A VAL* 3.2 4.3 + - - +
456A ALA* 2.9 26.2 + - - +
501A AJB 3.5 31.0 - - - +
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Residues in contact with SER 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A PHE* 3.9 18.6 - - - -
146A LEU 3.6 5.1 + - - -
147A GLY* 3.3 24.1 + - - -
200A VAL* 3.7 17.6 - - - +
201A ALA* 3.7 9.4 - - - +
449A ALA 3.0 20.0 + - - -
450A ALA* 3.5 7.0 - - - -
452A VAL* 1.3 79.0 - - - +
454A ALA* 1.3 52.0 + - - +
456A ALA* 3.0 2.1 + - - +
457A CYS* 2.7 38.8 + - - +
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Residues in contact with ALA 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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69A SER* 3.4 17.9 - - - +
70A GLU* 2.8 38.7 + - - +
74A PHE* 3.4 26.2 - - + -
91A VAL* 4.1 11.4 - - + -
98A GLN* 5.5 0.4 - - + -
450A ALA 2.8 17.7 + - - +
451A LEU* 3.6 6.3 - - - +
452A VAL 3.3 0.2 - - - -
453A SER* 1.3 74.2 - - - +
455A VAL* 1.3 60.7 + - - +
457A CYS* 3.7 3.9 - - - +
458A LYS 3.9 1.0 + - - -
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Residues in contact with VAL 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A PRO* 3.9 27.4 - - + +
68A GLY 4.2 8.5 - - - +
69A SER* 3.7 20.0 - - - -
98A GLN* 4.5 1.1 - - - +
215A TYR* 4.4 4.3 - - - +
451A LEU 3.4 6.0 + - - +
452A VAL 3.2 7.5 + - - +
453A SER 3.1 0.6 - - - -
454A ALA* 1.3 76.0 - - - +
456A ALA* 1.3 63.3 + - - +
457A CYS 3.1 2.0 - - - -
458A LYS* 3.1 19.9 + - - +
459A LYS* 4.4 2.4 + - - +
501A AJB 3.5 55.0 - - + +
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Residues in contact with ALA 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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159A ILE* 4.9 8.7 - - + -
200A VAL* 3.4 30.5 - - + +
201A ALA* 4.6 5.4 - - + -
452A VAL 2.9 16.3 + - - +
453A SER* 4.2 0.2 - - - -
455A VAL* 1.3 76.8 - - - +
457A CYS* 1.3 61.3 + - - +
459A LYS* 3.2 16.0 + - - +
460A ALA* 3.2 14.0 + - - +
501A AJB 4.2 17.9 - - + -
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Residues in contact with CYS 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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70A GLU* 3.8 14.4 - - + +
74A PHE* 4.0 5.6 - - - -
145A PRO* 3.9 18.6 - - - -
198A ASP* 5.4 0.2 - - - -
200A VAL* 3.8 24.0 - - - -
453A SER 2.7 20.5 + - - +
454A ALA* 3.7 9.4 - - - +
455A VAL 3.1 0.4 - - - -
456A ALA* 1.3 69.8 - - - +
458A LYS* 1.3 56.2 + - - +
459A LYS 2.9 6.1 + - - -
460A ALA 4.1 0.9 - - - +
461A CYS* 2.8 64.8 + - + +
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Residues in contact with LYS 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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68A GLY* 3.6 26.7 - - - +
69A SER 4.0 11.0 + - - -
70A GLU* 2.5 44.7 + - - +
454A ALA 3.9 2.7 + - - +
455A VAL 3.1 18.1 + - - +
457A CYS* 1.3 76.3 - - - +
459A LYS* 1.3 65.4 + - + +
461A CYS 4.5 4.3 - - - +
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Residues in contact with LYS 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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455A VAL 5.4 1.6 - - - +
456A ALA* 3.2 8.7 + - - +
457A CYS 2.9 0.4 - - - -
458A LYS* 1.3 87.8 - - + +
460A ALA* 1.3 57.6 + - + +
461A CYS 3.7 2.2 - - - -
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Residues in contact with ALA 460 (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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198A ASP* 4.0 13.7 - - - +
200A VAL* 5.3 12.3 - - + +
456A ALA 3.2 14.5 + - - +
457A CYS* 4.5 1.1 - - - -
459A LYS* 1.3 79.0 - - - +
461A CYS* 1.3 60.8 + - - +
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Residues in contact with CYS 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A GLU* 4.9 14.8 - - + +
145A PRO* 4.8 9.4 - - - -
198A ASP* 4.8 7.4 - - - +
457A CYS* 2.8 51.0 + - + +
458A LYS* 4.5 5.4 - - - +
459A LYS 3.7 1.2 - - - -
460A ALA* 1.3 81.5 + - - +
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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
------------------------------------------------------------
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