Contacts of the helix formed by residues 74 - 89 (chain D) in PDB entry 3F0D
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 ASP 74 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38D ASP* 3.6 9.8 - - - +
72D GLY 3.5 2.7 + - - -
73D ALA* 1.3 69.6 - - - +
75D SER* 1.3 59.3 + - - +
76D ARG* 2.9 30.4 + - - +
77D ALA* 3.0 32.6 + - + +
78D LEU* 3.3 10.9 + - - +
80D ARG* 5.1 4.0 + - - -
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Residues in contact with SER 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D SER* 3.7 4.2 + - - -
38D ASP* 2.6 32.9 + - - -
40D ASP* 3.7 17.7 - - - -
43D LEU* 3.8 10.7 - - - +
44D HIS* 2.8 31.2 + - - -
47D THR* 5.2 0.5 + - - -
73D ALA 3.2 1.8 + - - -
74D ASP* 1.3 71.0 - - - +
76D ARG* 1.3 57.4 + - - +
77D ALA 3.3 0.2 - - - -
78D LEU* 3.4 12.4 + - - +
79D LEU* 2.9 27.9 + - - +
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Residues in contact with ARG 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D GLY* 3.9 24.2 + - - -
43D LEU* 3.5 19.9 - - + +
74D ASP* 2.9 15.8 + - - +
75D SER* 1.3 74.9 - - - +
77D ALA* 1.3 60.5 + - - +
79D LEU* 3.3 2.8 + - - +
80D ARG* 2.9 47.0 + - - +
117D ASN* 3.3 44.9 + - + +
120D ALA* 4.0 11.3 - - - +
121D ASP* 2.8 37.4 + - - +
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Residues in contact with ALA 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D ASP* 3.0 22.4 + - + +
76D ARG* 1.3 76.3 - - - +
78D LEU* 1.3 66.1 + - + +
80D ARG* 3.3 25.3 + - - +
81D GLU* 3.0 23.7 + - - +
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Residues in contact with LEU 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D SER* 4.6 6.7 - - - -
44D HIS* 4.5 11.2 - - + +
47D THR* 4.8 3.1 - - - +
59D ILE* 5.1 6.3 - - + -
63D PHE* 3.5 42.7 - - + -
70D PHE* 3.8 34.5 - - + -
73D ALA* 4.5 14.8 - - + -
74D ASP 3.3 9.3 + - - +
75D SER* 3.6 24.7 - - - +
76D ARG 3.3 0.6 - - - -
77D ALA* 1.3 80.7 - - + +
79D LEU* 1.3 56.8 + - - +
81D GLU* 3.2 1.5 + - - -
82D CYS* 2.8 28.6 + - - +
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Residues in contact with LEU 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D LEU* 4.1 28.0 - - + +
46D ILE* 4.1 13.0 - - + -
47D THR* 3.5 25.2 + - - +
50D LEU* 3.9 16.8 - - + -
75D SER 2.9 17.6 + - - +
76D ARG* 3.6 6.3 - - - +
78D LEU* 1.3 74.4 - - - +
80D ARG* 1.3 57.8 + - - +
82D CYS* 3.3 4.8 + - - +
83D ALA* 2.9 26.9 + - - +
118D ILE* 4.6 11.2 - - + -
121D ASP* 3.9 23.1 - - + +
122D LEU* 3.9 26.7 - - + -
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Residues in contact with ARG 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D ASP* 5.1 4.6 + - - -
76D ARG* 2.9 39.2 + - - +
77D ALA* 3.6 26.8 - - - +
79D LEU* 1.3 75.7 - - - +
81D GLU* 1.3 58.3 + - - +
83D ALA* 3.3 4.7 + - - +
84D SER* 3.0 26.9 + - - -
120D ALA 5.5 0.2 - - - -
121D ASP* 3.0 52.7 + - + +
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Residues in contact with GLU 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D PHE* 3.8 14.8 - - + -
77D ALA 3.0 17.6 + - - +
78D LEU* 3.7 4.0 - - - +
80D ARG* 1.3 74.9 - - - +
82D CYS* 1.3 65.0 + - - +
84D SER* 3.2 14.0 + - - -
85D ARG* 2.8 68.8 + - - +
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Residues in contact with CYS 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D THR* 3.7 37.5 - - + -
50D LEU* 3.7 28.0 - - - -
51D PHE* 3.6 33.8 - - + -
63D PHE* 4.1 1.2 - - + -
78D LEU 2.8 14.3 + - - +
79D LEU* 3.4 8.3 - - - +
81D GLU* 1.3 76.5 - - - +
83D ALA* 1.3 57.8 + - - +
85D ARG* 3.1 4.2 + - - +
86D VAL* 2.9 32.6 + - - +
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Residues in contact with ALA 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D LEU* 5.3 0.4 - - - -
79D LEU 2.9 16.7 + - - +
80D ARG* 3.6 7.4 - - - +
81D GLU 3.3 0.2 - - - -
82D CYS* 1.3 78.6 - - - +
84D SER* 1.3 57.6 + - - +
86D VAL* 3.4 8.1 + - - +
87D ALA* 3.0 29.3 + - - +
93D ILE* 4.4 11.7 - - + +
121D ASP 4.5 5.8 - - - +
122D LEU* 3.8 26.2 - - + +
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Residues in contact with SER 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D ARG 3.0 13.7 + - - -
81D GLU* 3.4 23.0 + - - -
82D CYS 3.2 0.2 - - - -
83D ALA* 1.3 77.0 - - - +
85D ARG* 1.3 58.0 + - - +
87D ALA* 3.4 7.8 + - - +
88D GLN* 2.9 31.8 + - - +
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Residues in contact with ARG 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D PHE* 4.3 11.9 - - + -
56D LEU* 3.9 9.0 - - + +
62D HIS* 3.0 58.7 + - + +
63D PHE* 4.0 10.6 - - - -
69D ARG* 6.1 1.2 - - - +
81D GLU* 2.8 53.4 + - - +
82D CYS 3.6 5.8 - - - +
84D SER* 1.3 74.8 - - - +
86D VAL* 1.3 65.5 + - - +
88D GLN* 3.2 9.0 + - - +
89D ALA* 2.9 23.0 + - - +
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Residues in contact with VAL 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D LEU* 3.8 29.6 - - + +
51D PHE* 4.4 2.9 - - + -
54D ALA* 4.2 11.9 - - + -
56D LEU* 4.1 12.6 - - + -
82D CYS* 2.9 29.7 + - - +
83D ALA* 3.7 7.4 - - - +
85D ARG* 1.3 75.4 - - - +
87D ALA* 1.3 61.9 + - - +
89D ALA* 3.2 10.4 + - - +
90D GLY 3.3 0.5 + - - -
91D PHE* 3.1 43.0 + - + +
93D ILE* 4.6 17.3 - - + -
156D VAL* 4.7 7.4 - - + -
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Residues in contact with ALA 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D ALA 3.0 17.8 + - - +
84D SER* 3.7 7.4 - - - +
85D ARG 3.2 0.2 - - - -
86D VAL* 1.3 75.6 - - - +
88D GLN* 1.3 59.0 + - - +
90D GLY* 2.9 21.0 + - - -
91D PHE 3.4 15.3 - - - +
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Residues in contact with GLN 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D SER* 2.9 19.6 + - - +
85D ARG* 3.2 12.5 + - + +
87D ALA* 1.3 76.3 - - - +
89D ALA* 1.3 59.6 + - - +
90D GLY* 3.4 1.0 + - - -
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Residues in contact with ALA 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D LEU* 4.0 27.8 - - + -
85D ARG 2.9 12.5 + - - +
86D VAL 3.5 9.4 - - - +
87D ALA 3.1 0.2 - - - -
88D GLN* 1.3 76.9 - - - +
90D GLY* 1.3 57.2 + - - +
91D PHE* 3.7 23.2 - - + -
158D ARG* 4.9 6.9 + - - -
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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