Contacts of the helix formed by residues 99 - 116 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E ASP* 3.0 43.7 - - + +
341E ILE* 4.4 8.1 - - + -
98L LYS* 1.3 89.2 - - + +
100L ARG* 1.3 66.8 + - - +
101L PHE* 3.3 41.1 - - + -
102L HIS* 3.0 29.8 + - + +
103L LYS* 3.2 11.5 + - - +
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Residues in contact with ARG 100 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C GLY* 2.4 50.1 - - - +
144E ALA 5.8 3.1 - - - +
145E SER 4.4 2.7 - - - -
146E GLY* 3.8 30.6 + - - -
148E THR* 4.4 0.4 - - - +
99L MET* 1.3 72.8 - - - +
101L PHE* 1.3 67.1 + - + +
103L LYS* 3.0 15.0 + - - +
104L ILE* 3.0 28.4 + - + +
127L GLU* 3.9 15.0 + - - +
130L VAL* 4.3 15.6 - - + +
131L ASP* 2.6 41.2 + - - -
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Residues in contact with PHE 101 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C GLN* 5.5 0.6 - - - +
23E GLY* 5.8 1.8 - - - -
24E ASP 5.3 4.0 - - - -
25E ASP* 4.7 1.3 - - - -
143E TYR* 4.9 6.5 - - + +
144E ALA 4.9 8.1 - - - -
341E ILE* 3.8 15.0 - - + -
344E SER* 5.5 2.7 - - - -
345E ILE* 1.9 71.8 - - + -
348E SER* 5.4 0.7 - - - -
349E LEU* 4.4 4.9 - - - +
99L MET* 3.3 40.4 - - + -
100L ARG* 1.3 80.8 - - + +
102L HIS* 1.3 102.7 + + - +
104L ILE* 3.5 13.0 + - + +
105L ALA* 3.0 23.0 + - - +
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Residues in contact with HIS 102 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E GLY* 4.3 24.2 + - - -
25E ASP* 4.6 2.6 + - - -
348E SER* 5.2 5.6 + - - -
95L ASP* 4.5 18.5 + - + +
96L LYS 3.4 19.2 + - - +
97L GLY* 3.5 31.3 - - - +
99L MET* 3.0 46.9 + - + +
101L PHE* 1.3 100.3 - + - +
103L LYS* 1.3 59.9 + - + +
105L ALA* 3.4 6.1 + - - +
106L ASN* 3.0 34.7 + - - +
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Residues in contact with LYS 103 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74L ARG* 3.7 48.4 - - + +
75L ASN* 3.7 33.6 - - + +
98L LYS* 3.6 25.9 + - - +
99L MET 3.5 9.6 - - - +
100L ARG* 3.0 11.1 + - - +
102L HIS* 1.3 75.2 - - + +
104L ILE* 1.3 60.5 + - - +
106L ASN* 3.2 1.0 + - - +
107L VAL* 2.8 35.2 + - - +
130L VAL* 3.8 20.8 + - + +
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Residues in contact with ILE 104 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C GLY* 2.9 20.9 - - - -
49C GLN* 1.6 83.5 - - + +
50C LYS* 5.0 1.1 - - + -
349E LEU* 6.3 0.7 - - + -
100L ARG* 3.0 24.2 + - + +
101L PHE* 3.7 11.2 - - - +
103L LYS* 1.3 74.9 - - - +
105L ALA* 1.3 59.8 + - - +
107L VAL 3.5 0.7 + - - -
108L ASN* 2.9 40.5 + - - +
126L ALA* 3.9 8.9 - - + +
127L GLU* 5.1 2.7 - - - -
130L VAL* 3.7 20.6 - - + +
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Residues in contact with ALA 105 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349E LEU* 3.1 37.0 - - + +
95L ASP* 4.2 17.5 - - - +
101L PHE 3.0 12.6 + - - +
102L HIS* 3.6 5.4 - - - +
103L LYS 3.2 0.2 - - - -
104L ILE* 1.3 78.7 - - - +
106L ASN* 1.3 62.9 + - - +
108L ASN* 3.3 8.1 + - - +
109L LYS* 3.1 28.4 + - - +
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Residues in contact with ASN 106 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75L ASN 3.7 18.1 + - - +
76L GLY* 4.6 3.1 - - - -
77L LEU* 4.1 14.3 - - - +
80L MET* 3.5 17.4 - - - +
94L PRO* 3.2 9.5 - - - +
95L ASP* 2.7 47.1 + - - +
97L GLY 5.3 1.6 + - - -
102L HIS* 3.0 23.4 + - - +
103L LYS* 5.1 0.2 - - - +
105L ALA* 1.3 73.4 - - - +
107L VAL* 1.3 65.1 + - - +
109L LYS* 3.0 30.4 + - - +
110L ALA 3.3 8.5 + - - -
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Residues in contact with VAL 107 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74L ARG 3.8 15.3 - - - +
76L GLY* 3.7 23.6 - - - +
79L LEU* 4.7 4.5 - - + -
103L LYS 2.8 23.4 + - - +
104L ILE 4.0 2.7 - - - +
106L ASN* 1.3 73.1 - - - +
108L ASN* 1.3 57.5 + - - +
110L ALA* 3.3 6.6 + - - +
111L LEU* 2.9 35.4 + - + +
126L ALA* 3.5 29.8 - - + -
129L ILE* 3.7 28.9 - - + -
130L VAL* 4.1 5.2 - - + -
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Residues in contact with ASN 108 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C GLN* 4.1 11.8 + - - +
51C ASP* 4.4 16.7 + - - +
52C SER* 5.4 2.6 - - - +
104L ILE* 2.9 33.9 + - - +
105L ALA* 3.6 7.7 - - - +
106L ASN 3.1 0.4 - - - -
107L VAL* 1.3 76.1 - - - +
109L LYS* 1.3 59.4 + - - +
111L LEU* 3.8 13.3 - - - +
112L ASP* 2.9 46.0 + - - +
126L ALA* 3.0 23.6 - - - +
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Residues in contact with LYS 109 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350E SER* 4.9 17.0 + - - +
80L MET* 3.8 20.0 - - + -
91L LEU* 4.4 3.3 - - - +
92L PRO* 4.4 28.1 - - + +
93L ARG 3.4 22.2 + - - +
95L ASP* 3.2 24.2 + - - -
105L ALA* 3.1 17.3 + - - +
106L ASN* 3.0 35.1 + - - +
108L ASN* 1.3 76.1 - - - +
110L ALA* 1.3 57.3 + - - +
112L ASP* 3.9 5.3 - - - +
113L PHE* 3.0 28.1 + - - +
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Residues in contact with ALA 110 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79L LEU* 3.7 26.7 - - + -
80L MET* 4.1 13.4 - - + +
83L LEU* 3.6 25.1 - - + +
91L LEU* 4.2 5.4 - - - -
106L ASN 3.3 3.4 + - - +
107L VAL* 3.5 7.6 - - - +
108L ASN 3.2 0.2 - - - -
109L LYS* 1.3 77.8 - - - +
111L LEU* 1.3 67.2 + - - +
113L PHE* 3.0 4.0 + - - +
114L ILE* 3.0 27.1 + - + +
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Residues in contact with LEU 111 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C SER* 4.2 3.1 - - - +
79L LEU* 5.4 0.7 - - + -
107L VAL* 2.9 25.7 + - + +
108L ASN* 3.8 16.2 - - - +
110L ALA* 1.3 72.5 - - - +
112L ASP* 1.3 60.5 + - - +
114L ILE* 3.4 7.3 + - + +
115L ALA* 2.9 28.6 + - - +
121L LEU* 3.7 21.0 - - + +
124L ILE* 4.1 22.4 - - + +
125L GLY 3.8 6.1 - - - +
126L ALA* 3.4 37.0 - - - +
129L ILE* 4.7 1.3 - - + -
140L MET* 3.8 29.4 - - + -
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Residues in contact with ASP 112 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108L ASN* 2.9 33.1 + - - +
109L LYS* 3.9 4.9 - - - +
111L LEU* 1.3 75.6 - - - +
113L PHE* 1.3 61.5 + - - +
115L ALA* 3.2 8.4 + - - +
116L SER* 2.8 31.3 + - - -
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Residues in contact with PHE 113 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83L LEU* 4.1 22.0 - - + -
87L SER* 3.7 21.8 - - - -
89L GLU* 3.8 21.8 - - + -
90L ARG 5.1 3.4 - - - -
91L LEU* 3.6 40.2 - - + -
92L PRO* 5.7 3.4 - - + -
109L LYS 3.0 16.6 + - - +
110L ALA 3.0 7.6 + - - +
112L ASP* 1.3 76.5 - - - +
114L ILE* 1.3 62.7 + - - +
116L SER* 2.5 28.1 + - - -
117L LYS* 3.4 29.2 + - - +
148L PHE* 3.7 23.6 - + - -
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Residues in contact with ILE 114 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79L LEU* 5.6 0.2 - - + -
83L LEU* 4.0 23.1 - - + -
110L ALA* 3.0 22.0 + - + +
111L LEU* 3.5 13.5 - - + +
113L PHE* 1.3 75.2 - - - +
115L ALA* 1.3 61.2 + - - +
117L LYS* 2.9 26.2 + - - +
119L VAL* 3.2 45.9 - - + +
121L LEU* 4.0 9.4 - - + -
140L MET* 4.5 14.8 - - + +
143L THR* 4.4 6.3 - - + +
144L ILE* 3.4 34.1 - - + -
148L PHE* 4.6 6.5 - - + -
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Residues in contact with ALA 115 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C LYS* 5.2 9.6 - - + -
111L LEU 2.9 13.3 + - - +
112L ASP* 3.6 9.4 - - - +
114L ILE* 1.3 75.8 - - - +
116L SER* 1.3 61.9 + - - +
117L LYS 3.1 1.0 + - - -
118L GLY* 3.1 12.3 + - - -
119L VAL 3.2 21.5 + - - +
121L LEU* 3.4 20.8 - - + +
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Residues in contact with SER 116 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112L ASP 2.8 13.4 + - - -
113L PHE* 2.5 30.5 + - - -
114L ILE 3.1 0.2 - - - -
115L ALA* 1.3 75.7 - - - +
117L LYS* 1.3 64.3 + - - +
118L GLY 3.1 4.2 + - - -
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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
------------------------------------------------------------
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