Contacts of the helix formed by residues 79 - 90 (chain Q) in PDB entry 3LEL
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 ILE 79 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75Q LYS* 5.4 11.0 - - + -
77Q ARG* 3.9 12.3 - - + +
78Q ILE* 1.3 89.1 - - - +
80Q PRO* 1.4 76.8 - - + +
81Q ARG* 3.6 26.2 - - + +
82Q HIS* 3.0 35.7 + - + +
83Q LEU* 3.5 2.1 + - - +
52R SER* 3.5 16.2 - - - +
55R ALA* 3.7 4.5 - - - -
59S C 6.4 2.0 - - - -
60S A 5.7 2.7 - - - +
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Residues in contact with PRO 80 (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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79Q ILE* 1.4 87.2 - - + +
81Q ARG* 1.3 67.3 + - - +
83Q LEU* 2.9 21.5 + - + +
84Q GLN* 3.2 8.8 + - - +
102Q ILE* 4.1 6.3 - - + +
103Q ALA 3.5 17.3 - - - +
104Q GLN* 3.4 23.6 - - + +
105Q GLY* 4.3 1.3 - - - -
52R SER* 3.8 9.9 - - - +
54R LYS* 3.8 20.2 - - + +
55R ALA* 3.7 21.8 - - + +
58R ILE* 4.5 6.3 - - + -
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Residues in contact with ARG 81 (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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55K GLN 3.4 15.2 + - - -
56K LYS* 3.8 21.9 + - - +
58K THR* 3.7 17.7 - - + +
73Q ASN* 5.5 2.9 - - - +
79Q ILE* 3.2 22.3 - - + +
80Q PRO* 1.3 81.0 - - - +
82Q HIS* 1.3 70.9 + - + +
84Q GLN* 3.0 13.7 + - - +
85Q LEU* 3.1 44.1 + - + +
104Q GLN 3.7 5.7 + - - +
105Q GLY 3.0 28.5 + - - -
106Q GLY* 3.4 4.4 - - - -
107Q VAL 2.9 37.9 + - - +
109Q PRO* 4.2 9.7 - - - +
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Residues in contact with HIS 82 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66Q ALA* 3.7 19.9 - - + +
69Q ALA* 3.9 9.4 - - + +
70Q ALA* 3.3 40.7 - - + +
73Q ASN* 4.1 20.7 + - - +
75Q LYS* 3.9 19.1 - - + +
77Q ARG 3.5 11.0 - - - -
78Q ILE* 3.5 7.3 - - + -
79Q ILE* 3.0 42.5 + - + +
81Q ARG* 1.3 89.9 - - + +
83Q LEU* 1.3 56.2 + - - +
85Q LEU* 3.6 6.0 + - + +
86Q ALA* 3.0 29.6 + - - +
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Residues in contact with LEU 83 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62Q ILE* 4.0 21.1 - - + +
63Q LEU* 5.0 4.0 - - + -
66Q ALA* 3.6 23.6 - - + -
78Q ILE* 4.0 8.3 - - + -
79Q ILE 4.0 7.4 - - - +
80Q PRO* 2.9 9.2 + - + +
82Q HIS* 1.3 77.9 - - - +
84Q GLN* 1.3 51.6 + - - +
86Q ALA* 3.2 1.4 + - - +
87Q VAL* 2.7 42.0 + - + +
102Q ILE* 4.2 13.0 - - + -
51R ILE* 5.7 0.4 - - + -
55R ALA* 3.7 34.3 - - + +
58R ILE* 3.7 24.5 - - + -
59R MET* 4.3 15.5 - - + -
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Residues in contact with GLN 84 (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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80Q PRO 3.2 2.6 + - - +
81Q ARG* 3.0 7.9 + - - +
83Q LEU* 1.3 75.9 - - - +
85Q LEU* 1.3 56.5 + - - +
87Q VAL* 4.4 0.4 - - - -
88Q ARG* 2.6 78.0 + - + +
102Q ILE* 3.4 31.9 + - + +
105Q GLY* 3.3 35.4 - - - +
106Q GLY 3.3 20.1 + - - +
107Q VAL* 4.6 10.2 - - - +
108Q LEU* 5.2 1.3 - - + -
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Residues in contact with LEU 85 (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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69Q ALA* 4.3 15.0 - - + -
73Q ASN* 4.1 23.8 - - - +
81Q ARG* 3.1 55.2 + - + +
82Q HIS* 3.8 10.5 - - + +
84Q GLN* 1.3 78.5 - - + +
86Q ALA* 1.3 56.9 + - - +
89Q ASN* 3.0 44.6 + - - +
108Q LEU* 3.9 20.9 - - + -
109Q PRO* 4.6 7.0 - - + -
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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
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62Q ILE* 4.3 6.1 - - + +
65Q LEU* 3.6 20.0 - - + +
66Q ALA* 3.4 32.8 - - + +
69Q ALA* 4.6 1.1 - - - +
82Q HIS 3.0 18.8 + - - +
83Q LEU* 3.4 4.3 - - - +
85Q LEU* 1.3 74.5 - - - +
87Q VAL* 1.3 69.9 + - + +
89Q ASN* 4.8 0.2 - - - +
90Q ASP* 3.7 20.3 + - - +
93Q LEU* 4.3 5.9 - - - +
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Residues in contact with VAL 87 (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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62Q ILE* 4.1 23.8 - - + -
83Q LEU* 2.7 24.4 + - + +
84Q GLN 3.8 1.3 - - - +
86Q ALA* 1.3 75.3 - - - +
88Q ARG* 1.3 93.2 + - - +
90Q ASP 3.1 17.2 - - - +
93Q LEU* 3.9 10.7 - - + +
94Q ASN 3.3 12.2 + - - +
97Q LEU* 3.7 35.0 - - + -
102Q ILE* 4.2 13.7 - - + -
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Residues in contact with ARG 88 (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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84Q GLN* 2.6 63.5 + - + +
87Q VAL* 1.3 89.4 - - - +
89Q ASN* 1.3 59.0 + - - +
90Q ASP 3.3 5.9 + - - +
91Q GLU* 5.5 0.2 - - - -
94Q ASN* 2.9 41.8 + - - +
97Q LEU* 3.0 24.8 + - - +
98Q GLY* 4.4 4.4 + - - -
100Q VAL* 3.0 29.7 + - - +
101Q THR* 5.0 1.0 - - - +
102Q ILE* 4.7 4.2 - - - +
108Q LEU* 3.7 29.2 - - + +
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Residues in contact with ASN 89 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85Q LEU* 3.0 30.3 + - - +
86Q ALA 4.5 0.7 - - - +
87Q VAL 3.4 0.2 - - - -
88Q ARG* 1.3 77.8 - - - +
90Q ASP* 1.3 57.7 + - - +
91Q GLU 4.1 0.9 + - - -
108Q LEU* 3.5 39.0 - - - +
109Q PRO* 5.8 1.4 - - - +
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Residues in contact with ASP 90 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61Q GLU* 6.1 0.7 - - - -
65Q LEU* 4.4 14.8 - - + -
86Q ALA 3.7 14.8 + - - +
87Q VAL 3.1 14.5 + - - +
88Q ARG 3.2 2.4 - - - -
89Q ASN* 1.3 78.6 - - - +
91Q GLU* 1.3 67.3 + - - +
92Q GLU* 3.2 18.9 + - - +
93Q LEU* 2.8 43.3 + - - +
94Q ASN* 3.3 10.2 + - - +
103R LEU* 6.1 0.2 - - - +
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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