Contacts of the helix formed by residues 81 - 99 (chain Q) 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 SER 81 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B GLU* 4.3 16.7 + - - -
228B ASP* 5.6 0.2 - - - -
77Q LEU 3.3 16.1 - - - +
78Q ASN 3.9 5.4 - - - -
79Q SER 3.5 0.8 - - - -
80Q ILE* 1.4 84.3 + - - +
82Q LYS* 1.4 62.7 + - - +
83Q ALA* 3.7 12.1 + - - -
84Q LYS* 3.4 34.4 + - - +
85Q ALA 3.6 8.3 + - - -
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Residues in contact with LYS 82 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B GLU* 3.3 33.5 + - - -
185B GLU* 3.3 26.2 - - + +
229B TYR* 6.0 0.2 - - - +
78Q ASN* 4.2 10.5 + - + +
81Q SER* 1.4 69.8 - - - +
83Q ALA* 1.3 64.6 + - - +
85Q ALA* 3.1 8.3 + - - +
86Q ALA* 3.0 23.9 + - - +
120Q GLU* 3.7 43.4 + - - +
122Q ARG* 3.5 9.7 + - - +
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Residues in contact with ALA 83 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B GLU* 3.4 12.0 + - - -
225B GLU* 4.3 3.8 - - + +
228B ASP* 3.8 26.6 - - + +
229B TYR* 3.5 36.4 + - + +
232B ALA* 5.4 2.1 - - - +
81Q SER* 3.4 7.8 - - - -
82Q LYS* 1.3 79.5 - - - +
84Q LYS* 1.4 55.8 + - - +
86Q ALA* 3.4 3.4 + - - +
87Q ARG* 3.0 27.4 + - - +
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Residues in contact with LYS 84 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B THR* 4.1 24.4 - - - +
225B GLU* 4.3 8.9 - - - +
228B ASP* 3.3 32.0 + - - +
43Q VAL* 4.7 8.3 - - + -
47Q GLU* 5.6 3.4 - - - +
77Q LEU* 4.0 13.5 - - + -
80Q ILE* 4.3 23.0 - - + +
81Q SER* 3.4 28.9 + - - +
82Q LYS 3.4 0.6 - - - -
83Q ALA* 1.4 70.2 - - - +
85Q ALA* 1.4 59.4 + - - +
87Q ARG* 3.2 25.6 + - - +
88Q LEU* 2.9 34.0 + - - +
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Residues in contact with ALA 85 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77Q LEU* 4.0 25.3 - - + +
78Q ASN* 3.6 30.7 - - - +
81Q SER 3.6 3.6 + - - -
82Q LYS* 3.1 14.4 + - - +
84Q LYS* 1.4 77.9 - - - +
86Q ALA* 1.3 68.9 + - - +
88Q LEU* 4.4 0.3 - - - +
89Q VAL* 3.4 27.9 + - + +
122Q ARG* 4.7 6.3 - - - +
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Residues in contact with ALA 86 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B GLU* 4.2 7.4 - - - +
232B ALA* 5.3 9.6 - - + -
82Q LYS 3.0 12.7 + - - +
83Q ALA 3.5 5.6 - - - +
85Q ALA* 1.3 83.3 - - - +
87Q ARG* 1.4 62.8 + - - +
89Q VAL* 3.8 3.4 - - - +
90Q ARG* 3.3 22.6 + - - +
122Q ARG* 3.8 24.7 - - - +
125Q LEU* 4.2 22.6 - - + +
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Residues in contact with ARG 87 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B ASP* 3.5 36.0 + - + +
231B ALA* 4.0 27.8 - - + -
232B ALA* 5.4 8.2 - - + +
43Q VAL* 5.5 2.4 - - - +
47Q GLU* 3.6 27.5 + - - +
83Q ALA 3.0 16.9 + - - +
84Q LYS* 3.2 27.7 + - - +
86Q ALA* 1.4 76.5 - - - +
88Q LEU* 1.4 84.6 + - - +
90Q ARG* 3.4 4.4 + - - +
91Q SER* 3.0 37.4 + - - +
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Residues in contact with LEU 88 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43Q VAL* 5.3 1.6 - - + +
46Q LYS* 3.8 29.2 - - + -
47Q GLU* 4.2 16.4 - - + +
50Q ILE* 3.7 33.9 - - + +
73Q VAL* 5.5 5.4 - - + -
77Q LEU* 3.9 27.1 - - + -
84Q LYS 2.9 18.2 + - - +
85Q ALA 4.6 0.4 - - - +
87Q ARG* 1.4 98.8 - - - +
89Q VAL* 1.4 63.1 + - + +
91Q SER* 3.6 6.9 - - - -
92Q LEU* 3.1 26.8 + - - +
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Residues in contact with VAL 89 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70Q LEU* 4.7 16.6 - - + +
73Q VAL* 5.6 7.9 - - + -
74Q ARG* 4.9 11.4 - - + -
77Q LEU* 5.8 5.4 - - + -
78Q ASN* 6.3 0.4 - - - +
85Q ALA* 3.4 20.3 + - + +
86Q ALA* 3.8 4.0 - - - +
87Q ARG 3.4 0.6 - - - -
88Q LEU* 1.4 76.6 - - + +
90Q ARG* 1.3 60.3 + - - +
92Q LEU* 3.9 2.0 - - - +
93Q LEU* 3.3 26.2 + - + +
113Q CYS* 3.5 32.3 - - - -
116Q TRP* 3.9 24.2 - - + -
125Q LEU* 6.1 2.2 - - + -
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Residues in contact with ARG 90 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B ALA 5.9 2.5 - - - +
232B ALA* 5.6 6.3 - - - +
86Q ALA 3.3 15.5 + - - +
87Q ARG* 3.9 4.7 - - - +
89Q VAL* 1.3 78.2 - - - +
91Q SER* 1.4 58.2 - - - +
93Q LEU* 3.4 11.0 + - - +
94Q ASP* 2.7 46.5 + - - +
125Q LEU* 4.3 23.8 - - + -
128Q ALA* 3.6 29.8 + - - +
129Q LEU* 3.8 35.0 - - - +
132Q ARG* 3.6 42.0 - - - +
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Residues in contact with SER 91 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B ALA* 6.0 0.5 - - - +
50Q ILE* 5.2 8.1 - - - -
87Q ARG* 3.0 29.0 + - - +
88Q LEU* 3.6 9.6 - - - -
90Q ARG* 1.4 75.7 - - - +
92Q LEU* 1.4 61.0 + - - +
94Q ASP* 3.4 17.3 + - - +
95Q LEU* 3.3 21.2 + - - +
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Residues in contact with LEU 92 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50Q ILE* 4.1 34.5 - - + +
53Q LEU* 4.3 15.0 - - + -
54Q GLY 6.1 0.2 - - - +
66Q LEU* 3.7 37.7 - - + +
69Q LEU* 5.5 3.6 - - + -
70Q LEU* 3.7 33.7 - - + +
73Q VAL* 6.0 3.4 - - + -
88Q LEU 3.1 16.2 + - - +
89Q VAL* 3.9 4.3 - - - +
91Q SER* 1.4 76.8 - - - +
93Q LEU* 1.3 64.7 + - - +
95Q LEU* 3.2 16.2 + - + +
96Q PHE* 3.1 20.7 + - - +
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Residues in contact with LEU 93 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66Q LEU* 6.0 0.4 - - + -
70Q LEU* 3.4 43.7 - - + -
89Q VAL* 3.3 16.8 + - + +
90Q ARG* 3.5 18.6 - - - +
92Q LEU* 1.3 81.0 - - + +
94Q ASP* 1.4 61.4 + - - +
96Q PHE* 3.2 23.6 - - + +
97Q LEU* 3.2 32.4 + - + +
106Q GLU* 5.0 2.7 - - + -
109Q LEU* 4.9 9.4 - - + +
110Q CYS* 3.9 29.8 - - - +
113Q CYS* 5.4 3.8 - - - -
129Q LEU* 5.4 10.5 - - + -
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Residues in contact with ASP 94 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90Q ARG* 2.7 41.1 + - - +
91Q SER* 3.7 9.4 - - - +
92Q LEU 3.3 0.2 - - - -
93Q LEU* 1.4 73.3 - - - +
95Q LEU* 1.4 63.3 + - + +
96Q PHE 3.4 0.5 + - - -
97Q LEU* 3.4 21.2 + - + +
98Q ASP* 3.5 17.3 - - - +
132Q ARG* 3.2 33.6 + - - +
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Residues in contact with LEU 95 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50Q ILE* 3.5 40.8 - - + +
51Q LEU* 5.6 4.9 - - + -
54Q GLY* 5.1 11.9 - - - -
57Q LEU* 4.0 10.4 - - + +
91Q SER* 3.3 18.2 - - - +
92Q LEU* 3.2 16.1 + - + +
94Q ASP* 1.4 78.5 - - + +
96Q PHE* 1.3 60.7 + - - +
98Q ASP* 3.6 24.5 - - - +
99Q MET* 3.8 15.4 - - + +
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Residues in contact with PHE 96 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57Q LEU* 4.4 10.3 - - + -
63Q ALA* 3.4 43.3 - - + -
66Q LEU* 3.7 29.1 - - + +
92Q LEU 3.1 13.0 + - - +
93Q LEU* 3.2 22.0 - - + +
95Q LEU* 1.3 77.9 - - - +
97Q LEU* 1.4 59.9 + - - +
98Q ASP 3.5 0.5 + - - -
99Q MET* 3.7 17.0 + - - +
101Q ALA* 4.5 14.7 - - + +
105Q GLN* 4.9 8.7 - - + -
106Q GLU* 3.7 36.3 - - + -
109Q LEU* 3.5 32.8 - - + -
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Residues in contact with LEU 97 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93Q LEU* 3.4 24.0 - - + +
94Q ASP* 3.4 18.6 - - + +
96Q PHE* 1.4 76.7 - - - +
98Q ASP* 1.3 72.8 + - - +
99Q MET 3.0 9.1 - - - +
101Q ALA* 5.5 0.2 - - - +
106Q GLU* 3.3 38.4 - - - +
132Q ARG* 3.7 51.4 - - + +
136Q LEU* 5.4 2.5 - - + -
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Residues in contact with ASP 98 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94Q ASP* 3.5 17.8 + - - +
95Q LEU* 3.6 20.9 - - - +
96Q PHE 3.3 0.4 - - - -
97Q LEU* 1.3 85.6 - - - +
99Q MET* 1.3 75.2 + - + +
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Residues in contact with MET 99 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54Q GLY* 3.9 23.1 - - - +
57Q LEU* 3.8 27.4 - - + +
58Q ALA* 3.7 33.0 - - + +
95Q LEU* 3.8 22.2 - - + +
96Q PHE 3.9 8.2 - - - +
97Q LEU 3.0 15.8 - - - +
98Q ASP* 1.3 88.4 - - + +
100Q GLU* 1.4 69.8 + - - +
101Q ALA* 3.5 4.9 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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