Contacts of the helix formed by residues 69 - 79 (chain A) in PDB entry 4JDL
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 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A HIS 4.6 1.3 - - - +
68A ALA* 1.3 84.7 - - + +
70A PRO* 1.3 64.1 - - + +
71A GLU* 4.1 7.2 - - + +
72A SER* 2.9 29.0 + - - +
73A VAL* 2.7 34.8 + - - +
71B GLU* 5.9 6.1 - - + +
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Residues in contact with PRO 70 (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 ALA 3.5 2.1 - - - +
69A PRO* 1.3 86.4 - - + +
71A GLU* 1.3 54.1 + - + +
73A VAL* 3.5 13.4 - - + +
74A TRP* 2.7 34.8 + - - +
132A HIS* 3.5 29.0 + - + +
154A LEU* 4.5 7.2 - - + +
164A VAL* 6.2 2.9 - - + -
306A GOL 4.7 26.0 - - - +
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Residues in contact with GLU 71 (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 PRO* 4.6 7.2 - - + -
70A PRO* 1.3 80.7 - - + +
72A SER* 1.3 60.3 + - - +
74A TRP* 3.0 22.3 + - - +
75A ALA* 3.1 15.4 + - - +
132A HIS* 4.0 8.5 + - + -
72B SER* 4.9 15.3 - - - +
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Residues in contact with SER 72 (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 ALA* 4.0 9.0 - - - -
69A PRO* 2.9 36.2 + - - +
71A GLU* 1.3 74.0 - - - +
73A VAL* 1.3 65.9 + - - +
75A ALA* 3.8 10.2 + - - +
76A LEU* 3.9 11.3 + - - +
200A THR* 4.5 10.0 + - - -
71B GLU* 4.9 16.2 + - - +
72B SER* 5.6 4.7 + - - +
75B ALA* 4.7 14.8 - - - +
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Residues in contact with VAL 73 (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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66A ILE* 3.6 46.9 - - + +
68A ALA* 3.8 9.9 - - + +
69A PRO 2.7 24.5 + - - +
70A PRO* 3.5 11.2 - - + +
72A SER* 1.3 76.0 - - - +
74A TRP* 1.3 62.1 + - - +
75A ALA 3.3 0.3 + - - -
76A LEU* 3.5 5.4 + - - +
77A VAL* 3.4 17.2 + - - +
154A LEU* 3.8 21.1 - - + -
164A VAL* 4.8 10.1 - - + -
196A LEU* 4.2 15.1 - - + +
200A THR* 4.8 7.6 - - + -
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Residues in contact with TRP 74 (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 PRO 2.7 22.6 + - - +
71A GLU* 3.0 6.7 + - - +
73A VAL* 1.3 73.6 - - - +
75A ALA* 1.3 55.8 + - - +
77A VAL* 3.1 32.4 + - + +
78A ARG* 2.5 63.3 + - + +
127A LEU* 3.6 15.9 - - + -
128A ASP 3.1 27.6 - - - -
129A GLU* 3.4 25.8 + - - +
132A HIS* 3.4 37.2 - + + +
133A VAL* 3.5 29.4 - - - -
134A ILE* 3.8 19.5 - - + -
152A THR 4.7 1.6 - - - -
154A LEU* 3.8 3.6 - - + -
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Residues in contact with ALA 75 (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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71A GLU 3.1 12.5 + - - +
72A SER* 4.1 6.7 - - - +
73A VAL 3.4 0.2 - - - -
74A TRP* 1.3 80.4 - - - +
76A LEU* 1.3 64.7 + - - +
77A VAL 3.1 0.3 + - - -
78A ARG* 3.3 12.7 + - - +
79A ARG* 3.2 25.0 + - - +
72B SER* 4.2 20.6 - - - +
75B ALA* 4.4 10.3 - - + -
76B LEU* 6.3 2.0 - - + -
200B THR* 5.3 9.0 - - + -
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Residues in contact with LEU 76 (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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72A SER 3.9 7.9 + - - +
73A VAL 3.5 9.3 + - - +
74A TRP 3.4 0.4 - - - -
75A ALA* 1.3 79.2 - - - +
77A VAL* 1.3 59.5 + - - +
79A ARG* 4.0 4.8 - - - +
85A VAL* 3.4 19.7 - - + +
86A TYR* 3.3 29.5 - - + -
196A LEU* 3.8 21.5 - - + +
199A SER* 4.5 18.6 - - - -
200A THR* 5.2 8.1 - - + -
75B ALA* 5.6 1.4 - - + +
79B ARG* 6.3 1.1 - - + -
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Residues in contact with VAL 77 (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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73A VAL 3.4 6.6 + - - +
74A TRP* 3.1 36.9 + - + +
76A LEU* 1.3 75.6 - - - +
78A ARG* 1.3 72.6 + - - +
79A ARG 3.0 11.3 + - - +
86A TYR* 3.3 36.3 + - + +
134A ILE* 3.4 18.5 - - + +
152A THR* 4.3 16.4 - - + -
154A LEU* 3.8 15.3 - - + -
193A LEU* 5.5 0.2 - - + -
196A LEU* 3.7 24.7 - - + -
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Residues in contact with ARG 78 (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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74A TRP* 2.5 49.1 + - + +
75A ALA* 3.6 8.1 + - - +
77A VAL* 1.3 76.7 - - - +
79A ARG* 1.3 85.2 + - - +
80A PHE* 2.7 25.6 + - - +
101A LEU 4.7 11.0 + - - +
127A LEU* 4.5 5.5 - - + +
129A GLU* 3.2 41.2 + - - +
134A ILE* 4.3 13.0 - - - +
199B SER* 3.0 43.8 + - - +
200B THR* 4.6 9.9 - - - +
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Residues in contact with ARG 79 (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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75A ALA* 3.2 20.4 - - - +
76A LEU* 4.0 4.3 - - - +
77A VAL 3.0 8.3 + - - +
78A ARG* 1.3 110.1 - - - +
80A PHE* 1.3 63.3 + - - +
81A ASP* 3.5 23.4 - - - +
82A ASN* 2.9 16.8 - - + +
83A PRO* 4.2 2.9 - - - +
85A VAL* 3.6 39.0 - - + +
86A TYR* 5.0 1.4 - - - -
101A LEU* 5.0 5.9 - - - +
76B LEU* 6.4 2.9 - - + -
85B VAL 5.6 3.6 + - - -
198B ARG* 4.2 15.2 - - - +
199B SER* 3.5 32.2 + - - +
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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