Contacts of the helix formed by residues 99 - 116 (chain Q) in PDB entry 3LUE
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 MET 99 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25H ASP* 3.0 42.2 - - + +
341H ILE* 4.4 8.5 - - + -
98Q LYS* 1.3 88.0 - - + +
100Q ARG* 1.3 68.5 + - - +
101Q PHE* 3.3 41.3 - - + -
102Q HIS* 3.0 29.2 + - + +
103Q LYS* 3.2 11.7 + - - +
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Residues in contact with ARG 100 (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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48F GLY* 2.4 50.7 - - - +
144H ALA 5.9 2.2 - - - +
145H SER 4.4 2.5 - - - -
146H GLY* 3.8 31.3 + - - -
148H THR* 4.4 0.4 - - - +
99Q MET* 1.3 72.7 - - - +
101Q PHE* 1.3 68.0 + - + +
103Q LYS* 3.0 14.8 + - - +
104Q ILE* 3.0 28.4 + - + +
127Q GLU* 3.9 14.1 + - - +
130Q VAL* 4.3 15.6 - - + +
131Q ASP* 2.6 41.2 + - - -
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Residues in contact with PHE 101 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49F GLN* 5.4 0.7 - - - +
23H GLY 5.8 1.8 - - - -
24H ASP 5.3 4.3 - - - -
25H ASP* 4.7 1.1 - - - -
143H TYR* 4.9 6.5 - - + +
144H ALA* 4.9 7.4 - - + -
341H ILE* 3.8 14.4 - - + -
344H SER* 5.5 2.9 - - - -
345H ILE* 1.9 72.9 - - + -
348H SER* 5.4 0.4 - - - -
349H LEU* 4.4 4.6 - - - +
99Q MET* 3.3 40.6 - - + -
100Q ARG* 1.3 80.0 - - + +
102Q HIS* 1.3 102.6 + + - +
104Q ILE* 3.5 13.1 + - + +
105Q ALA* 3.0 23.6 + - - +
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Residues in contact with HIS 102 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23H GLY* 4.3 24.0 + - - -
25H ASP* 4.7 3.0 + - - -
348H SER* 5.2 6.0 + - - -
349H LEU* 6.0 0.2 - - - -
95Q ASP* 4.5 17.4 + - + +
96Q LYS 3.4 19.6 + - - +
97Q GLY* 3.5 32.4 - - - +
98Q LYS 4.6 0.2 - - - -
99Q MET* 3.0 47.3 + - + +
101Q PHE* 1.3 99.3 - + - +
103Q LYS* 1.3 57.9 + - + +
105Q ALA* 3.4 6.9 + - - +
106Q ASN* 3.0 35.1 + - - +
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Residues in contact with LYS 103 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74Q ARG* 3.7 48.6 - - + +
75Q ASN* 3.7 32.7 - - + +
97Q GLY 5.7 0.7 - - - +
98Q LYS* 3.6 24.9 + - - +
99Q MET 3.5 10.3 - - - +
100Q ARG* 3.0 10.0 + - - +
102Q HIS* 1.3 75.8 - - + +
104Q ILE* 1.3 60.4 + - - +
106Q ASN* 3.8 0.7 - - - +
107Q VAL* 2.8 34.8 + - - +
130Q VAL* 3.8 20.1 + - + -
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Residues in contact with ILE 104 (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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48F GLY* 2.9 20.9 - - - -
49F GLN* 1.6 82.6 - - + +
50F LYS* 4.1 1.8 - - + +
349H LEU* 6.3 0.4 - - + -
100Q ARG* 3.0 25.3 + - + +
101Q PHE* 3.7 11.2 - - - +
103Q LYS* 1.3 75.2 - - - +
105Q ALA* 1.3 59.1 + - - +
107Q VAL 3.8 0.2 - - - -
108Q ASN* 2.9 41.1 + - - +
126Q ALA* 3.9 9.3 - - + +
127Q GLU* 5.1 3.1 - - - -
130Q VAL* 3.7 20.4 - - + -
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Residues in contact with ALA 105 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349H LEU* 3.1 35.4 - - + -
95Q ASP* 4.2 18.2 - - - +
101Q PHE 3.0 13.4 + - - +
102Q HIS* 3.6 5.6 - - - +
104Q ILE* 1.3 78.9 - - - +
106Q ASN* 1.3 62.1 + - - +
108Q ASN* 3.3 7.1 + - - +
109Q LYS* 3.1 28.1 + - - +
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Residues in contact with ASN 106 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75Q ASN 3.7 18.0 + - - +
76Q GLY* 4.6 3.1 - - - -
77Q LEU* 4.1 13.7 - - + +
80Q MET* 3.5 16.7 - - - +
94Q PRO* 3.2 9.3 - - - +
95Q ASP* 2.7 48.2 + - - +
97Q GLY 5.3 1.2 + - - -
102Q HIS* 3.0 23.0 + - - +
103Q LYS 3.2 0.4 + - - +
105Q ALA* 1.3 75.3 - - - +
107Q VAL* 1.3 64.7 + - - +
109Q LYS* 3.0 30.9 + - - +
110Q ALA 3.3 8.8 + - - -
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Residues in contact with VAL 107 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74Q ARG 3.8 15.7 - - - +
76Q GLY* 3.7 24.0 - - - +
79Q LEU* 4.7 4.7 - - + -
103Q LYS 2.8 23.1 + - - +
104Q ILE 4.0 2.7 - - - +
106Q ASN* 1.3 72.5 - - - +
108Q ASN* 1.3 57.0 + - - +
110Q ALA* 3.3 6.4 + - - +
111Q LEU* 2.9 35.2 + - + +
126Q ALA* 3.5 30.7 - - + -
129Q ILE* 3.7 27.8 - - + -
130Q VAL* 4.1 5.2 - - + -
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Residues in contact with ASN 108 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49F GLN* 4.1 12.1 + - - +
51F ASP* 4.4 15.9 + - - +
52F SER* 5.4 2.4 + - - +
104Q ILE* 2.9 33.5 + - - +
105Q ALA* 3.6 8.4 - - - +
106Q ASN 3.1 0.2 - - - -
107Q VAL* 1.3 75.4 - - - +
109Q LYS* 1.3 59.3 + - - +
111Q LEU* 3.8 13.2 - - - +
112Q ASP* 2.9 45.6 + - - +
126Q ALA* 3.0 24.6 - - - +
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Residues in contact with LYS 109 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350H SER* 4.9 17.2 - - - +
80Q MET* 3.8 19.7 - - + -
91Q LEU* 4.4 3.5 - - - +
92Q PRO* 4.4 27.5 - - + +
93Q ARG 3.4 22.0 + - - +
95Q ASP* 3.2 23.9 + - - -
105Q ALA* 3.1 16.7 + - - +
106Q ASN* 3.0 36.0 + - - +
108Q ASN* 1.3 76.8 - - - +
110Q ALA* 1.3 57.2 + - - +
112Q ASP* 3.9 4.9 - - - +
113Q PHE* 3.0 28.5 + - - +
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Residues in contact with ALA 110 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79Q LEU* 3.7 26.5 - - + -
80Q MET* 4.1 14.5 - - + +
83Q LEU* 3.6 24.2 - - + +
91Q LEU* 4.2 5.6 - - - -
106Q ASN 3.3 3.7 + - - +
107Q VAL 3.5 8.1 - - - +
108Q ASN 3.2 0.2 - - - -
109Q LYS* 1.3 76.9 - - - +
111Q LEU* 1.3 67.2 + - - +
113Q PHE* 3.0 4.2 + - - +
114Q ILE* 3.0 27.2 + - + +
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Residues in contact with LEU 111 (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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52F SER* 4.2 2.7 - - - +
79Q LEU* 5.4 0.4 - - + -
107Q VAL* 2.9 24.6 + - + +
108Q ASN* 3.8 16.4 - - - +
110Q ALA* 1.3 73.6 - - - +
112Q ASP* 1.3 60.0 + - - +
114Q ILE* 3.4 7.9 + - + +
115Q ALA* 2.9 28.6 + - - +
121Q LEU* 3.7 21.5 - - + +
124Q ILE* 4.1 22.9 - - + +
125Q GLY 3.8 5.2 - - - -
126Q ALA* 3.4 38.4 - - - +
129Q ILE* 4.7 1.3 - - + -
140Q MET* 3.8 30.1 - - + -
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Residues in contact with ASP 112 (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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108Q ASN* 2.9 34.9 + - - +
109Q LYS* 3.9 5.0 - - - +
111Q LEU* 1.3 75.0 - - - +
113Q PHE* 1.3 60.4 + - - +
115Q ALA* 3.2 7.8 + - - +
116Q SER* 2.8 31.8 + - - -
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Residues in contact with PHE 113 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83Q LEU* 4.1 22.0 - - + -
87Q SER* 3.7 21.8 - - - -
89Q GLU* 3.8 21.5 - - + -
90Q ARG 5.1 3.1 - - - -
91Q LEU* 3.6 40.8 - - + -
92Q PRO* 5.7 3.1 - - + -
109Q LYS 3.0 16.4 + - - +
110Q ALA 3.0 7.6 + - - +
112Q ASP* 1.3 77.0 - - - +
114Q ILE* 1.3 62.2 + - - +
116Q SER* 2.5 26.5 + - - -
117Q LYS* 3.4 29.5 + - - +
148Q PHE* 3.7 24.0 - + - -
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Residues in contact with ILE 114 (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 LEU* 5.6 0.2 - - + -
83Q LEU* 4.0 22.9 - - + -
110Q ALA* 3.0 22.7 + - + +
111Q LEU* 3.5 13.0 - - + +
113Q PHE* 1.3 75.6 - - - +
115Q ALA* 1.3 60.6 + - - +
117Q LYS* 2.9 25.1 + - - +
119Q VAL* 3.2 45.8 - - + +
121Q LEU* 4.0 10.3 - - + -
140Q MET* 4.5 13.7 - - + +
143Q THR* 4.4 6.1 - - + +
144Q ILE* 3.4 35.4 - - + -
148Q PHE* 4.6 6.3 - - + -
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Residues in contact with ALA 115 (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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68F LYS* 5.2 9.6 - - - -
111Q LEU 2.9 13.5 + - - +
112Q ASP* 3.6 9.9 - - - +
114Q ILE* 1.3 76.0 - - - +
116Q SER* 1.3 62.5 + - - +
117Q LYS 3.1 0.9 + - - -
118Q GLY* 3.1 12.0 + - - -
119Q VAL 3.2 21.2 + - - +
121Q LEU* 3.4 20.4 - - + +
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Residues in contact with SER 116 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112Q ASP 2.8 13.6 + - - -
113Q PHE* 2.5 29.4 + - - -
115Q ALA* 1.3 76.5 - - - +
117Q LYS* 1.3 62.5 + - - +
118Q GLY 3.1 4.3 + - - -
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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