Contacts of the helix formed by residues 67 - 82 (chain Z) in PDB entry 5LN3
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 67 (chain Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65Z GLU* 3.2 20.6 + - + +
66Z LYS* 1.4 78.9 - - - +
68Z THR* 1.3 74.1 + - - +
69Z SER* 3.4 29.5 + - - -
70Z LEU* 4.0 8.9 + - + +
71Z TYR* 3.4 19.9 + - - +
118Z ASN* 4.6 0.4 - - - -
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Residues in contact with THR 68 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66Z LYS 3.9 2.7 + - - -
67Z ASP* 1.3 80.3 - - - +
69Z SER* 1.4 80.1 + - - +
71Z TYR* 3.1 2.1 + - - +
72Z ARG* 3.0 63.0 + - - +
117Z GLU* 4.3 21.1 + - - +
118Z ASN* 5.2 2.7 - - - -
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Residues in contact with SER 69 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62Z ARG* 5.5 0.2 + - - -
67Z ASP* 3.3 14.9 + - - -
68Z THR* 1.4 84.5 - - - +
70Z LEU* 1.4 66.7 + - - +
72Z ARG* 4.7 1.6 - - - +
73Z PRO* 3.0 27.9 - - - +
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Residues in contact with LEU 70 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62Z ARG* 3.5 54.7 + - + +
65Z GLU* 4.7 17.5 - - + -
67Z ASP* 4.0 11.5 + - + +
68Z THR 3.5 0.2 - - - -
69Z SER* 1.4 87.8 - - - +
71Z TYR* 1.4 62.0 + - - +
72Z ARG 3.6 0.3 + - - -
73Z PRO* 3.7 2.9 - - - +
74Z ALA* 3.5 21.5 + - - +
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Residues in contact with TYR 71 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62Z ARG 3.7 20.8 + - - +
63Z LEU* 3.3 29.1 + - + -
65Z GLU 3.7 9.2 - - - +
67Z ASP 3.4 16.6 + - - +
68Z THR* 3.1 5.3 + - - +
70Z LEU* 1.4 78.4 - - - +
72Z ARG* 1.4 76.0 + - - +
74Z ALA* 3.7 1.0 - - - +
75Z LEU* 3.0 60.9 + - + +
106Z LEU* 4.1 5.7 - - - +
109Z ILE* 6.1 1.1 - - + +
118Z ASN* 3.6 42.8 - - - -
122Z ALA* 3.6 14.6 - - - +
125Z ILE* 3.5 24.9 - - + +
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Residues in contact with ARG 72 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68Z THR* 3.0 39.4 + - - +
69Z SER* 4.7 1.1 - - - +
71Z TYR* 1.4 111.6 - - - +
73Z PRO* 1.3 69.7 - - + +
74Z ALA 3.2 0.2 + - - -
75Z LEU* 3.3 5.9 + - - +
76Z GLU* 3.0 33.2 + - + +
117Z GLU* 4.0 26.3 + - - +
118Z ASN* 4.2 5.5 - - - +
120Z ARG* 5.4 0.4 - - - +
121Z PHE* 3.5 57.9 - - - +
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Residues in contact with PRO 73 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62Z ARG* 5.0 17.7 - - - +
69Z SER 3.0 28.9 - - - +
70Z LEU 3.7 4.5 - - - +
72Z ARG* 1.3 83.1 - - + +
74Z ALA* 1.4 56.0 + - - +
76Z GLU* 3.4 8.9 + - + +
77Z GLU* 3.0 32.0 + - - +
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Residues in contact with ALA 74 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59Z LEU* 4.3 18.0 - - + +
62Z ARG* 3.7 28.2 - - + +
63Z LEU* 4.1 18.8 - - + +
70Z LEU 3.5 18.2 + - - +
71Z TYR 3.7 4.3 - - - +
72Z ARG 3.2 0.4 - - - -
73Z PRO* 1.4 74.9 - - - +
75Z LEU* 1.3 58.3 + - - +
77Z GLU* 3.5 7.2 - - - +
78Z LEU* 3.0 26.5 + - - +
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Residues in contact with LEU 75 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63Z LEU* 4.2 2.5 - - + -
71Z TYR* 3.0 57.6 + - + +
72Z ARG* 3.6 9.4 - - - +
74Z ALA* 1.3 73.6 - - - +
76Z GLU* 1.4 71.0 + - - +
78Z LEU* 3.1 14.3 + - + +
79Z ARG* 3.3 34.9 + - - +
121Z PHE* 3.7 38.4 - - + +
125Z ILE* 3.9 32.8 - - + -
150Z GLU* 6.1 1.3 - - + -
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Residues in contact with GLU 76 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72Z ARG* 3.0 30.2 + - + +
73Z PRO* 3.8 9.2 - - + +
75Z LEU* 1.4 78.2 - - - +
77Z GLU* 1.3 57.0 + - - +
79Z ARG* 3.3 10.2 + - - +
80Z ARG* 3.1 33.1 + - + +
121Z PHE* 4.8 8.3 - - - -
150Z GLU* 3.4 39.9 - - - +
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Residues in contact with GLU 77 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59Z LEU* 3.8 22.0 - - + -
73Z PRO 3.0 17.9 + - - +
74Z ALA* 3.5 7.2 - - - +
76Z GLU* 1.3 77.3 - - - +
78Z LEU* 1.4 55.0 + - - +
80Z ARG* 3.2 16.7 + - - +
81Z GLN* 2.9 36.2 + - - +
86Z THR* 5.0 19.4 - - - +
88Z SER* 5.6 1.8 + - - +
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Residues in contact with LEU 78 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59Z LEU* 3.9 27.1 - - + -
63Z LEU* 4.0 13.0 - - + -
74Z ALA 3.0 12.5 + - - +
75Z LEU* 3.1 13.0 + - + +
77Z GLU* 1.4 72.3 - - - +
79Z ARG* 1.4 74.7 + - - +
81Z GLN* 3.2 24.6 - - + +
82Z ILE* 3.3 17.3 - - + +
99Z LEU* 3.9 31.9 - - + -
125Z ILE* 3.7 38.1 - - + -
128Z VAL* 4.9 5.4 - - + -
129Z LEU* 5.3 4.0 - - + -
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Residues in contact with ARG 79 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75Z LEU* 3.3 26.2 + - - +
76Z GLU* 3.3 8.0 + - - +
78Z LEU* 1.4 98.8 - - - +
80Z ARG* 1.4 64.7 + - + +
82Z ILE* 3.4 11.7 + - - +
83Z ARG* 3.9 7.2 + - - +
121Z PHE* 6.1 2.0 - - - -
124Z ASP* 3.5 25.9 - - - +
125Z ILE* 4.0 3.8 - - - +
128Z VAL* 3.7 25.9 - - - +
148Z GLN 5.3 1.0 + - - -
149Z GLU* 3.0 28.2 + - - -
150Z GLU* 3.4 38.8 + - + +
151Z LEU 3.6 15.5 - - - +
152Z ALA* 3.2 24.9 - - + +
158Z TYR* 3.6 13.0 - - - -
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Residues in contact with ARG 80 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76Z GLU* 3.1 23.3 + - + +
77Z GLU* 3.2 22.4 + - - +
79Z ARG* 1.4 77.5 - - + +
81Z GLN* 1.3 59.6 + - - +
83Z ARG* 3.3 56.1 + - - +
84Z SER 3.8 3.5 + - - +
154Z TRP* 4.0 21.8 - - - -
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Residues in contact with GLN 81 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59Z LEU* 3.4 25.9 - - - +
77Z GLU* 2.9 22.0 + - - +
78Z LEU* 3.2 28.8 - - + +
80Z ARG* 1.3 71.7 - - - +
82Z ILE* 1.3 67.3 + - + +
83Z ARG 3.1 3.6 + - - -
84Z SER 3.6 8.1 - - - -
85Z SER* 3.2 25.6 + - - -
86Z THR* 2.9 42.7 + - - +
87Z THR* 3.1 18.0 + - - -
95Z PRO* 3.5 18.9 - - + +
99Z LEU* 4.2 11.4 - - + +
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Residues in contact with ILE 82 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78Z LEU* 3.3 21.8 - - + +
79Z ARG* 3.4 17.0 - - - +
80Z ARG 3.2 0.6 - - - -
81Z GLN* 1.3 81.0 - - + +
83Z ARG* 1.3 59.2 + - - +
85Z SER* 5.6 0.2 - - - -
95Z PRO* 6.3 2.2 - - + -
96Z LEU* 5.6 10.8 - - + -
128Z VAL* 5.8 6.5 - - + -
152Z ALA* 4.2 8.5 - - + -
153Z SER* 3.1 23.3 - - - +
156Z HIS* 3.4 18.5 + - + +
158Z TYR* 4.1 20.6 - - + -
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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