Contacts of the helix formed by residues 70 - 83 (chain D) in PDB entry 3CUQ
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 PRO 70 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17D PHE 3.5 15.9 - - - +
18D THR* 5.7 2.9 - - + -
19D LEU 5.9 0.4 - - - +
68D LYS* 3.0 11.6 - - + +
69D LEU* 1.3 88.2 - - + +
71D VAL* 1.3 66.4 + - - +
72D GLU* 4.4 6.3 - - + +
73D SER* 2.9 34.3 + - - +
74D ILE* 2.9 10.0 + - - +
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Residues in contact with VAL 71 (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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51D VAL* 4.0 19.2 - - + +
55D GLN* 3.2 40.4 - - + +
69D LEU 3.5 2.0 + - - +
70D PRO* 1.3 71.1 - - - +
72D GLU* 1.3 69.8 + - + +
74D ILE* 3.0 24.7 + - + +
75D GLN* 3.4 12.4 + - + +
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Residues in contact with GLU 72 (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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207A GLU* 6.0 6.2 - - + +
211A GLN* 4.8 16.6 + - - +
70D PRO* 3.1 6.3 - - + +
71D VAL* 1.3 80.5 - - + +
73D SER* 1.3 61.8 + - - +
75D GLN* 3.2 22.8 + - - +
76D ILE* 3.7 11.3 - - - +
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Residues in contact with SER 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D LEU* 3.8 33.3 + - - +
69D LEU* 3.2 30.4 - - - +
70D PRO* 2.9 20.4 + - - +
72D GLU* 1.3 74.3 - - - +
74D ILE* 1.3 64.0 + - - +
75D GLN 3.1 2.0 - - - -
76D ILE* 3.2 19.9 + - - +
77D VAL* 3.4 14.0 + - - +
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Residues in contact with ILE 74 (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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51D VAL* 5.3 14.6 - - + +
54D ALA* 5.3 6.3 - - + -
55D GLN* 5.8 7.4 - - + +
60D PHE* 3.5 50.7 - - + -
69D LEU* 3.5 24.0 - - + +
70D PRO 2.9 19.6 + - - +
71D VAL* 3.0 21.0 + - + +
73D SER* 1.3 76.1 - - - +
75D GLN* 1.3 59.2 + - + +
77D VAL* 3.0 23.5 - - - +
78D LEU* 3.1 31.3 + - + +
97D PHE* 6.4 0.2 - - + -
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Residues in contact with GLN 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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51D VAL* 4.2 17.3 - - + +
71D VAL* 3.4 13.4 + - + +
72D GLU* 3.2 12.9 + - - +
73D SER 3.1 0.8 - - - -
74D ILE* 1.3 81.7 - - + +
76D ILE* 1.3 65.9 + - + +
78D LEU* 4.0 6.4 - - - +
79D GLU* 3.4 21.1 + - - +
89D TRP* 3.3 40.3 - - - -
94D LYS* 4.2 22.3 + - - +
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Residues in contact with ILE 76 (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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19D LEU* 4.5 24.9 - - + -
26D ARG* 5.9 2.7 - - - +
30D LEU* 4.1 19.1 - - + -
72D GLU 3.7 14.8 - - - +
73D SER* 3.6 12.6 - - - +
74D ILE 3.2 1.0 - - - -
75D GLN* 1.3 82.4 - - + +
77D VAL* 1.3 65.0 + - - +
78D LEU 3.1 1.8 + - - -
79D GLU* 3.2 14.7 + - + +
80D GLU* 3.3 22.9 + - - +
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Residues in contact with VAL 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D LEU* 6.1 0.2 - - - +
30D LEU* 4.5 15.0 - - + +
33D TRP* 3.9 37.9 - - + +
34D CYS* 4.4 7.1 - - - +
37D VAL* 5.1 1.3 - - + -
60D PHE* 4.4 15.0 - - + -
69D LEU* 4.4 13.5 - - + -
73D SER 3.4 11.8 + - - +
74D ILE* 3.0 25.6 - - - +
76D ILE* 1.3 77.3 - - - +
78D LEU* 1.3 57.1 + - + +
80D GLU* 3.8 4.5 + - - +
81D LEU* 3.1 35.8 + - + +
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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 VAL* 5.9 1.6 - - + -
51D VAL* 5.3 5.8 - - + -
60D PHE* 5.0 8.1 - - + -
74D ILE* 3.1 39.6 + - + +
75D GLN* 4.0 18.6 - - - +
76D ILE 3.1 0.2 - - - -
77D VAL* 1.3 83.3 - - + +
79D GLU* 1.3 53.1 + - - +
81D LEU* 2.8 25.2 + - + +
82D ARG* 2.8 36.2 + - - +
87D LEU* 4.4 21.0 - - + +
89D TRP* 4.8 14.4 - - + +
97D PHE* 4.5 30.7 - - + -
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Residues in contact with GLU 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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75D GLN 3.4 11.5 + - - +
76D ILE* 3.2 12.2 + - - +
78D LEU* 1.3 77.4 - - - +
80D GLU* 1.3 53.9 + - + +
82D ARG* 2.7 45.5 + - - +
83D LYS* 2.8 55.4 + - - +
89D TRP* 5.5 5.5 + - - +
94D LYS* 5.0 9.2 + - - -
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Residues in contact with GLU 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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30D LEU* 3.7 33.9 - - + +
34D CYS* 4.3 14.8 - - - -
76D ILE* 3.3 20.3 - - - +
77D VAL 3.9 6.3 - - - +
78D LEU 3.2 0.2 - - - -
79D GLU* 1.3 76.1 - - + +
81D LEU* 1.3 58.0 + - - +
83D LYS* 3.7 29.3 + - - +
84D LYS* 3.1 32.3 + - + +
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Residues in contact with LEU 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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34D CYS* 4.2 21.3 - - + +
37D VAL* 3.2 44.6 - - + -
38D LEU* 5.2 7.2 - - + -
60D PHE* 6.3 0.4 - - + -
77D VAL* 3.1 23.2 + - + +
78D LEU* 2.8 27.0 + - + +
80D GLU* 1.3 75.8 - - - +
82D ARG* 1.3 51.2 + - - +
84D LYS* 4.1 8.5 - - + +
85D GLY 2.2 28.5 - - - +
86D ASN* 3.6 13.7 - - + +
87D LEU* 3.5 12.4 - - + +
99D ILE* 4.4 17.0 - - + -
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Residues in contact with ARG 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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78D LEU 2.8 9.9 + - - +
79D GLU* 2.7 36.9 + - - +
81D LEU* 1.3 76.9 - - - +
83D LYS* 1.3 69.6 + - - +
84D LYS 3.0 4.7 - - - -
85D GLY* 2.9 20.4 + - - -
87D LEU* 3.5 38.9 - - + +
88D GLU* 4.4 5.2 - - + +
89D TRP* 3.9 27.5 - - - +
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Residues in contact with LYS 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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79D GLU* 2.8 47.5 + - - +
80D GLU* 3.7 38.0 + - - +
82D ARG* 1.3 83.4 - - - +
84D LYS* 1.3 55.4 + - - +
85D GLY 3.3 2.2 - - - -
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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