Contacts of the helix formed by residues 70 - 81 (chain D) in PDB entry 3DLX
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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61D VAL* 3.6 18.4 - - + -
62D GLY* 3.4 20.6 - - - +
68D GLY 4.2 0.9 - - - +
69D ILE* 1.4 81.5 - - + +
71D GLU* 1.3 56.9 + - - +
73D LEU* 4.2 5.8 - - + -
74D ILE* 3.0 32.4 + - + +
209D LEU* 3.4 30.3 - - + +
210D VAL 4.0 3.4 - - - +
211D LYS* 3.7 14.6 - - + +
244D GLU* 2.9 26.5 - - + +
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Residues in contact with GLU 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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66D LEU 5.3 1.0 - - - +
69D ILE* 3.0 34.6 + - + +
70D PRO* 1.3 72.9 - - - +
72D ASN* 1.3 61.0 + - - +
74D ILE* 3.7 7.4 + - - +
75D ASP* 3.2 26.2 + - - +
97D PHE* 3.5 26.9 - - + -
101D LEU* 5.7 2.3 - - - +
244D GLU* 3.2 3.0 + - - -
274D LYS 4.5 2.3 - - - +
275D TYR* 3.8 21.2 - - + -
276D GLU* 2.9 31.7 + - - +
277D LYS* 3.0 27.9 + - - +
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Residues in contact with ASN 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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46D PRO* 4.1 12.1 - - + +
71D GLU* 1.3 78.0 - - - +
73D LEU* 1.3 63.0 + - - +
75D ASP* 3.5 6.8 + - - +
76D ALA* 3.1 24.6 + - - +
244D GLU* 3.0 23.7 + - - +
270D ILE* 4.4 14.6 - - + -
272D GLY* 3.4 12.9 - - - -
273D GLU* 3.8 10.5 + - - +
274D LYS* 3.0 30.5 + - - +
275D TYR* 3.1 18.2 + - - -
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Residues in contact with LEU 73 (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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46D PRO* 4.5 8.7 - - + +
49D ALA* 4.7 2.0 - - + -
50D VAL* 4.0 13.2 - - + -
70D PRO* 4.2 3.6 - - + +
72D ASN* 1.3 75.4 - - - +
74D ILE* 1.3 63.0 + - - +
76D ALA* 3.2 11.6 + - - +
77D LEU* 3.2 19.9 + - - +
209D LEU* 4.1 27.8 - - + -
210D VAL 4.0 4.0 - - - +
242D VAL* 3.3 52.0 - - + +
244D GLU* 2.7 36.2 + - + +
270D ILE* 4.1 20.4 - - + -
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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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61D VAL* 4.4 14.6 - - + -
69D ILE* 4.9 4.7 - - + -
70D PRO* 3.0 40.9 + - + +
71D GLU* 3.9 6.5 - - - +
73D LEU* 1.3 75.9 - - - +
75D ASP* 1.3 62.2 + - - +
77D LEU* 3.4 9.1 + - - +
78D LEU* 3.3 17.5 + - - +
98D GLY* 3.6 43.3 - - - +
99D LEU* 3.9 9.4 - - + +
101D LEU* 3.8 23.6 - - + -
102D LEU* 3.7 17.8 - - + +
209D LEU* 4.7 6.5 - - + +
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Residues in contact with ASP 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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71D GLU 3.2 18.7 + - - +
72D ASN* 3.6 8.5 - - - +
73D LEU 3.2 0.2 - - - -
74D ILE* 1.3 78.8 - - - +
76D ALA* 1.3 60.9 + - - +
78D LEU* 3.4 26.4 + - + +
79D LYS* 3.4 39.8 + - - +
101D LEU* 5.8 2.8 - - + +
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Residues in contact with ALA 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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46D PRO* 3.4 39.3 - - + +
47D VAL* 3.8 12.2 - - + +
50D VAL* 3.7 7.0 - - + -
72D ASN 3.1 13.4 + - - +
73D LEU* 3.2 10.0 + - - +
75D ASP* 1.3 76.7 + - - +
77D LEU* 1.3 59.7 + - - +
79D LYS* 3.3 6.2 + - - +
80D THR* 3.0 32.3 + - - +
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Residues in contact with LEU 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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50D VAL* 3.4 37.9 - - + +
53D ILE* 4.1 13.2 - - + -
59D VAL* 4.9 4.5 - - + -
73D LEU 3.2 11.5 + - - +
74D ILE* 3.6 9.2 - - - +
75D ASP 3.3 0.4 - - - -
76D ALA* 1.3 73.6 - - - +
78D LEU* 1.3 58.5 - - - +
79D LYS 3.2 0.7 - - - -
80D THR* 3.4 6.1 + - - +
81D GLY 3.1 15.9 + - - -
82D VAL* 3.9 14.4 - - + -
85D LEU* 4.1 17.9 - - + -
102D LEU* 3.9 26.9 - - + -
107D GLN* 2.8 22.6 + - - +
209D LEU* 3.8 21.8 - - + -
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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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74D ILE 3.3 14.5 + - - +
75D ASP* 3.5 24.2 - - - +
76D ALA 3.3 0.6 - - - -
77D LEU* 1.3 78.6 - - - +
79D LYS* 1.3 61.3 + - + +
81D GLY* 3.8 7.8 + - - -
101D LEU* 3.7 41.5 - - + +
102D LEU* 3.9 5.8 - - + -
105D SER* 3.5 34.8 - - - +
107D GLN* 3.7 6.7 - - - +
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Residues in contact with LYS 79 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47D VAL* 4.0 22.4 - - + -
75D ASP* 3.4 34.1 + - - +
76D ALA* 3.3 8.5 + - - +
77D LEU 3.2 0.4 - - - -
78D LEU* 1.3 75.9 - - + +
80D THR* 1.3 64.1 + - - +
81D GLY* 3.2 2.5 + - - -
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Residues in contact with THR 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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47D VAL* 4.4 20.0 - - + +
50D VAL* 4.1 24.6 + - + +
51D LYS* 4.8 8.3 - - - -
76D ALA 3.0 17.7 + - - +
77D LEU* 3.4 9.0 + - - +
78D LEU 3.6 0.2 - - - -
79D LYS* 1.3 76.9 - - - +
81D GLY* 1.3 63.2 + - - +
82D VAL* 3.2 25.7 + - - +
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Residues in contact with GLY 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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55D ASP* 4.5 1.0 - - - +
77D LEU 3.1 11.0 + - - -
78D LEU 3.8 7.1 + - - -
79D LYS 3.2 4.7 - - - -
80D THR* 1.3 78.2 - - - +
82D VAL* 1.3 65.3 + - - +
83D LYS* 3.5 8.7 + - - +
107D GLN* 3.8 10.6 - - - +
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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