Contacts of the helix formed by residues 99 - 116 (chain N) 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 N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25G ASP* 3.0 43.3 - - + +
341G ILE* 4.4 9.0 - - + -
98N LYS* 1.3 88.1 - - + +
100N ARG* 1.3 67.1 + - - +
101N PHE* 3.3 40.4 - - + -
102N HIS* 3.0 30.3 + - + +
103N LYS* 3.2 12.2 + - - +
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Residues in contact with ARG 100 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E MET 3.8 0.4 - - - -
48E GLY* 2.4 49.8 - - - +
144G ALA 5.9 2.5 - - - +
145G SER 4.4 2.9 - - - -
146G GLY* 3.8 31.1 + - - -
148G THR* 4.4 0.6 - - - +
98N LYS 3.9 0.2 + - - -
99N MET* 1.3 71.8 - - - +
101N PHE* 1.3 68.0 + - + +
103N LYS* 3.0 15.2 + - - +
104N ILE* 3.0 27.6 + - + +
127N GLU* 3.9 14.8 + - - +
130N VAL* 4.3 16.8 - - + +
131N ASP* 2.6 41.0 + - - -
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Residues in contact with PHE 101 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E GLN* 5.6 0.5 - - - +
23G GLY* 5.8 1.3 - - - -
24G ASP 5.3 4.3 - - - -
25G ASP* 4.7 1.6 - - - -
143G TYR* 4.9 6.7 - - + +
144G ALA 4.9 7.4 - - - -
341G ILE* 3.8 13.7 - - + -
344G SER* 5.5 2.9 - - - -
345G ILE* 1.9 73.8 - - + +
348G SER* 5.4 0.7 - - - -
349G LEU* 4.4 4.8 - - - +
99N MET* 3.3 40.4 - - + -
100N ARG* 1.3 81.0 - - + +
102N HIS* 1.3 102.0 + + - +
104N ILE* 3.5 13.1 + - + +
105N ALA* 3.0 23.4 + - - +
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Residues in contact with HIS 102 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G GLY* 4.3 24.5 + - - -
24G ASP 6.3 0.2 - - - -
25G ASP* 4.7 3.0 + - - -
348G SER* 5.2 6.0 + - - -
95N ASP* 4.5 17.2 + - + +
96N LYS 3.4 20.0 + - - +
97N GLY* 3.5 31.8 - - - +
98N LYS* 4.7 0.2 - - - -
99N MET* 3.0 47.2 + - + +
101N PHE* 1.3 99.3 - + - +
103N LYS* 1.3 57.6 + - + +
105N ALA* 3.4 6.8 + - - +
106N ASN* 3.0 34.5 + - - +
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Residues in contact with LYS 103 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74N ARG* 3.7 48.8 - - + +
75N ASN* 3.7 31.4 - - + +
97N GLY 5.7 0.7 - - - +
98N LYS* 3.6 25.9 + - - +
99N MET 3.5 9.4 - - - +
100N ARG* 3.0 11.3 + - - +
102N HIS* 1.3 76.6 - - + +
104N ILE* 1.3 58.8 + - - +
106N ASN* 3.2 0.9 + - - +
107N VAL* 2.8 35.3 + - - +
130N VAL* 3.8 19.9 + - + +
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Residues in contact with ILE 104 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E GLY* 2.9 20.6 - - - -
49E GLN* 1.6 84.1 - - + +
50E LYS* 4.1 1.8 - - + +
100N ARG* 3.0 25.3 + - + +
101N PHE* 3.7 11.2 - - - +
102N HIS 3.4 0.2 - - - -
103N LYS* 1.3 75.0 - - - +
105N ALA* 1.3 59.1 + - - +
107N VAL 3.8 0.2 - - - -
108N ASN* 2.9 41.5 + - - +
126N ALA* 3.9 9.8 - - + +
127N GLU* 5.1 2.7 - - - -
130N VAL* 3.7 20.6 - - + -
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Residues in contact with ALA 105 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349G LEU* 3.1 34.3 - - + -
95N ASP* 4.2 18.2 - - - +
101N PHE 3.0 13.2 + - - +
102N HIS* 3.6 5.6 - - - +
103N LYS 3.2 0.2 - - - -
104N ILE* 1.3 79.3 - - - +
106N ASN* 1.3 62.8 + - - +
108N ASN* 3.3 7.5 + - - +
109N LYS* 3.1 28.3 + - - +
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Residues in contact with ASN 106 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75N ASN 3.7 17.9 + - - +
76N GLY* 4.6 3.4 - - - -
77N LEU* 4.1 13.7 - - - +
80N MET* 3.5 16.5 - - - +
94N PRO* 3.2 9.5 - - - +
95N ASP* 2.7 47.2 + - - +
97N GLY 5.3 1.4 + - - -
102N HIS* 3.0 22.6 + - - +
103N LYS 3.2 0.4 + - - +
105N ALA* 1.3 74.9 - - - +
107N VAL* 1.3 64.3 + - - +
109N LYS* 3.0 31.8 + - - +
110N ALA 3.3 8.1 + - - -
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Residues in contact with VAL 107 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74N ARG 3.8 15.0 - - - +
76N GLY* 3.7 23.6 - - - -
79N LEU* 4.7 4.9 - - + -
103N LYS 2.8 23.0 + - - +
104N ILE 4.0 2.5 - - - +
106N ASN* 1.3 72.7 - - - +
108N ASN* 1.3 58.0 + - - +
110N ALA* 3.3 6.6 + - - +
111N LEU* 2.9 34.6 + - + +
126N ALA* 3.5 29.8 - - + -
129N ILE* 3.7 28.3 - - + -
130N VAL* 4.1 5.2 - - + -
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Residues in contact with ASN 108 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E GLN* 4.1 12.5 + - - +
51E ASP* 4.4 16.0 + - - +
52E SER* 5.4 2.4 - - - +
104N ILE* 2.9 32.7 + - - +
105N ALA* 3.6 7.7 - - - +
106N ASN 3.1 0.2 - - - -
107N VAL* 1.3 76.5 - - - +
109N LYS* 1.3 60.0 + - + +
111N LEU* 3.8 13.8 - - - +
112N ASP* 2.9 44.9 + - - +
126N ALA* 3.0 24.4 - - - +
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Residues in contact with LYS 109 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350G SER* 4.9 17.4 + - - +
80N MET* 3.8 19.7 - - + -
91N LEU* 4.4 2.9 - - - +
92N PRO* 4.4 28.0 - - + +
93N ARG 3.4 21.6 + - - +
95N ASP* 3.2 24.1 + - - -
105N ALA* 3.1 16.2 + - - +
106N ASN* 3.0 35.8 + - - +
108N ASN* 1.3 77.2 - - - +
110N ALA* 1.3 57.7 + - - +
112N ASP* 3.9 4.9 - - - +
113N PHE* 3.0 28.2 + - - +
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Residues in contact with ALA 110 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79N LEU* 3.7 26.0 - - + -
80N MET* 4.1 14.3 - - + +
83N LEU* 3.6 26.0 - - + +
91N LEU* 4.2 6.3 - - - -
106N ASN 3.3 3.1 + - - +
107N VAL* 3.5 7.6 - - - +
108N ASN 3.2 0.2 - - - -
109N LYS* 1.3 77.0 - - - +
111N LEU* 1.3 66.1 + - - +
113N PHE* 3.1 4.2 + - - +
114N ILE* 3.0 27.5 + - + +
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Residues in contact with LEU 111 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E SER* 4.2 2.9 - - - +
79N LEU* 5.4 0.2 - - + -
107N VAL* 2.9 26.1 + - + +
108N ASN* 3.8 15.7 - - - +
110N ALA* 1.3 73.9 - - - +
112N ASP* 1.3 60.4 + - - +
114N ILE* 3.4 9.1 + - + +
115N ALA* 2.9 28.1 + - - +
121N LEU* 3.7 21.1 - - + +
124N ILE* 4.1 22.2 - - + +
125N GLY 3.8 5.2 - - - +
126N ALA* 3.4 37.7 - - - +
129N ILE* 4.7 0.9 - - + -
140N MET* 3.8 29.8 - - + -
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Residues in contact with ASP 112 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108N ASN* 2.9 34.0 + - - +
109N LYS* 3.9 4.7 - - - +
111N LEU* 1.3 74.9 - - - +
113N PHE* 1.3 62.6 + - - +
115N ALA* 3.2 8.5 + - - +
116N SER* 2.8 31.5 + - - -
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Residues in contact with PHE 113 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83N LEU* 4.1 22.4 - - + -
87N SER* 3.7 21.8 - - - -
89N GLU* 3.8 21.5 - - + -
90N ARG 5.1 2.5 - - - -
91N LEU* 3.6 40.6 - - + -
92N PRO* 5.7 3.1 - - + -
109N LYS 3.0 15.3 + - - +
110N ALA 3.1 7.8 + - - +
112N ASP* 1.3 76.3 - - - +
114N ILE* 1.3 61.4 + - - +
116N SER* 2.5 27.1 + - - -
117N LYS* 3.4 28.9 + - - +
148N PHE* 3.7 23.6 - + - -
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Residues in contact with ILE 114 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83N LEU* 4.0 23.6 - - + -
110N ALA* 3.0 22.0 + - + +
111N LEU* 3.5 13.9 - - + +
113N PHE* 1.3 75.7 - - - +
115N ALA* 1.3 60.6 + - - +
117N LYS* 2.9 25.1 + - - +
119N VAL* 3.2 45.3 - - + +
121N LEU* 4.0 9.9 - - + -
140N MET* 4.5 13.9 - - + +
143N THR* 4.4 7.0 - - + +
144N ILE* 3.4 35.0 - - + -
148N PHE* 4.6 6.1 - - + -
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Residues in contact with ALA 115 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E LYS* 5.2 9.4 - - - -
111N LEU 2.9 13.3 + - - +
112N ASP* 3.6 9.9 - - - +
114N ILE* 1.3 76.6 - - - +
116N SER* 1.3 61.3 + - - +
117N LYS 3.0 1.3 + - - -
118N GLY* 3.1 12.1 + - - -
119N VAL 3.2 20.3 + - - +
121N LEU* 3.4 21.3 - - + +
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Residues in contact with SER 116 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112N ASP 2.8 14.7 + - - -
113N PHE* 2.5 30.1 + - - -
115N ALA* 1.3 75.8 - - - +
117N LYS* 1.3 63.2 + - - +
118N GLY 3.1 4.6 + - - -
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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