Contacts of the helix formed by residues 99 - 116 (chain S) 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 S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25J ASP* 3.0 43.3 - - + +
341J ILE* 4.4 8.1 - - + -
98S LYS* 1.3 89.8 - - + +
100S ARG* 1.3 67.0 + - - +
101S PHE* 3.3 41.7 - - + -
102S HIS* 3.0 29.4 + - + +
103S LYS* 3.2 11.5 + - - +
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Residues in contact with ARG 100 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H GLY* 2.4 50.0 - - - +
144J ALA 5.9 2.5 - - - +
145J SER 4.5 2.7 - - - -
146J GLY* 3.8 31.1 + - - -
148J THR* 4.3 0.6 - - - +
98S LYS 3.9 0.2 + - - -
99S MET* 1.3 73.7 - - - +
101S PHE* 1.3 68.5 + - + +
103S LYS* 3.0 14.5 + - - +
104S ILE* 3.0 29.8 + - + +
127S GLU* 3.9 16.0 + - - +
130S VAL* 4.3 15.0 - - + +
131S ASP* 2.6 41.2 + - - -
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Residues in contact with PHE 101 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49H GLN* 5.5 1.1 - - - +
23J GLY* 5.8 2.2 - - - -
24J ASP 5.3 4.0 - - - -
25J ASP* 4.7 1.1 - - - -
143J TYR* 4.9 6.7 - - + +
144J ALA* 4.9 7.6 - - - -
341J ILE* 3.8 14.1 - - + -
344J SER* 5.6 2.5 - - - -
345J ILE* 1.9 72.5 - - + -
348J SER* 5.4 0.4 - - - -
349J LEU* 4.4 4.7 - - - +
99S MET* 3.3 40.8 - - + -
100S ARG* 1.3 80.7 - - + +
102S HIS* 1.3 102.6 + + - +
104S ILE* 3.5 13.7 + - + +
105S ALA* 3.0 23.0 + - - +
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Residues in contact with HIS 102 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23J GLY* 4.3 24.1 + - - -
25J ASP* 4.7 3.6 + - - -
348J SER* 5.2 5.6 + - - -
95S ASP* 4.5 18.2 + - + +
96S LYS 3.4 19.8 + - - +
97S GLY* 3.5 31.1 - - - +
99S MET* 3.0 47.4 + - + +
101S PHE* 1.3 99.9 - + - +
103S LYS* 1.3 58.5 + - + +
105S ALA* 3.4 6.6 + - - +
106S ASN* 3.0 34.9 + - - +
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Residues in contact with LYS 103 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74S ARG* 3.7 47.3 - - + +
75S ASN* 3.7 32.7 - - + +
98S LYS* 3.6 26.3 + - - +
99S MET 3.2 9.4 + - - +
100S ARG* 3.0 11.1 + - - +
102S HIS* 1.3 75.5 - - + +
104S ILE* 1.3 59.9 + - - +
106S ASN* 3.2 1.6 + - - +
107S VAL* 2.8 34.8 + - - +
130S VAL* 3.8 20.1 + - + +
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Residues in contact with ILE 104 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H GLY* 2.9 20.2 - - - -
49H GLN* 1.6 83.2 - - + +
50H LYS* 5.0 1.8 - - + -
349J LEU* 6.3 0.4 - - + -
100S ARG* 3.0 25.3 + - + +
101S PHE* 3.7 11.0 - - - +
103S LYS* 1.3 74.7 - - - +
105S ALA* 1.3 59.8 + - - +
107S VAL 3.8 0.5 - - - -
108S ASN* 2.9 40.7 + - - +
126S ALA* 3.9 9.2 - - + +
127S GLU* 5.1 2.5 - - - -
130S VAL* 3.7 21.5 - - + +
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Residues in contact with ALA 105 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349J LEU* 3.1 35.7 - - + -
95S ASP* 4.2 17.5 - - - +
101S PHE 3.0 12.8 + - - +
102S HIS* 3.6 5.6 - - - +
103S LYS 3.2 0.2 - - - -
104S ILE* 1.3 78.4 - - - +
106S ASN* 1.3 62.4 + - - +
108S ASN* 3.3 7.7 + - - +
109S LYS* 3.1 28.9 + - - +
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Residues in contact with ASN 106 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75S ASN 3.7 18.2 + - - +
76S GLY* 4.6 2.7 - - - -
77S LEU* 4.1 14.3 - - + +
80S MET* 3.5 16.1 - - - +
94S PRO* 3.2 9.9 - - - +
95S ASP* 2.7 47.5 + - - +
97S GLY 5.3 1.6 + - - -
102S HIS* 3.0 23.2 + - - +
105S ALA* 1.3 73.5 - - - +
107S VAL* 1.3 65.5 + - - +
109S LYS* 3.0 31.3 + - - +
110S ALA 3.3 7.4 + - - -
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Residues in contact with VAL 107 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74S ARG 3.8 15.0 - - - +
76S GLY* 3.7 24.7 - - - +
79S LEU* 4.7 5.2 - - + -
103S LYS 2.8 23.0 + - - +
104S ILE 4.0 2.2 - - - +
106S ASN* 1.3 72.5 - - - +
108S ASN* 1.3 58.0 + - - +
110S ALA* 3.3 6.0 + - - +
111S LEU* 2.9 36.0 + - + +
126S ALA* 3.5 29.8 - - + -
129S ILE* 3.7 28.3 - - + -
130S VAL* 4.1 4.9 - - + -
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Residues in contact with ASN 108 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49H GLN* 4.2 12.0 + - - +
51H ASP* 4.4 15.8 + - - +
52H SER* 5.4 2.4 - - - +
104S ILE* 2.9 32.6 + - - +
105S ALA* 3.6 8.2 - - - +
106S ASN 3.1 0.4 - - - -
107S VAL* 1.3 76.7 - - - +
109S LYS* 1.3 59.8 + - - +
111S LEU* 3.8 13.8 - - - +
112S ASP* 2.9 46.4 + - - +
126S ALA* 3.0 23.8 - - - +
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Residues in contact with LYS 109 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350J SER* 4.9 17.2 + - - +
80S MET* 3.8 19.5 - - + -
91S LEU* 4.4 3.4 - - - +
92S PRO* 4.4 28.4 - - + +
93S ARG 3.4 21.8 + - - +
95S ASP* 3.2 23.7 + - - -
105S ALA* 3.1 16.7 + - - +
106S ASN* 3.0 35.5 + - - +
108S ASN* 1.3 76.4 - - - +
110S ALA* 1.3 58.0 + - - +
112S ASP* 3.9 4.2 - - - +
113S PHE* 3.0 28.6 + - - +
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Residues in contact with ALA 110 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79S LEU* 3.7 26.2 - - + -
80S MET* 4.1 13.4 - - + +
83S LEU* 3.6 25.8 - - + -
91S LEU* 4.2 5.6 - - - -
106S ASN 3.3 3.7 + - - +
107S VAL* 3.5 8.1 - - - +
108S ASN 3.2 0.2 - - - -
109S LYS* 1.3 77.4 - - - +
111S LEU* 1.3 66.8 + - - +
113S PHE* 3.0 4.2 + - - +
114S ILE* 3.0 27.1 + - + +
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Residues in contact with LEU 111 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52H SER* 4.2 3.1 - - - +
79S LEU* 5.4 0.7 - - + -
107S VAL* 2.9 26.6 + - + +
108S ASN* 3.8 15.9 - - - +
110S ALA* 1.3 73.5 - - - +
112S ASP* 1.3 60.0 + - - +
114S ILE* 3.4 7.4 + - + +
115S ALA* 2.9 28.8 + - - +
121S LEU* 3.7 21.0 - - + +
124S ILE* 4.1 21.5 - - + +
125S GLY 3.8 6.3 - - - -
126S ALA* 3.4 36.8 - - - +
129S ILE* 4.7 0.9 - - + -
140S MET* 3.8 29.6 - - + -
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Residues in contact with ASP 112 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108S ASN* 2.9 33.3 + - - +
109S LYS* 3.9 5.1 - - - +
111S LEU* 1.3 76.7 - - - +
113S PHE* 1.3 61.6 + - - +
115S ALA* 3.2 8.2 + - - +
116S SER* 2.8 31.3 + - - -
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Residues in contact with PHE 113 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83S LEU* 4.1 22.0 - - + -
87S SER* 3.7 20.6 - - - -
89S GLU* 3.8 22.4 - - + -
90S ARG 5.1 2.7 - - - -
91S LEU* 3.6 41.3 - - + -
92S PRO* 5.7 2.9 - - + -
109S LYS 3.0 16.0 + - - +
110S ALA 3.0 7.4 + - - +
112S ASP* 1.3 76.7 - - - +
114S ILE* 1.3 63.1 + - - +
116S SER* 2.5 27.4 + - - -
117S LYS* 3.4 28.6 + - - +
148S PHE* 3.7 24.2 - + - -
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Residues in contact with ILE 114 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83S LEU* 4.0 22.2 - - + -
110S ALA* 3.0 22.9 + - + +
111S LEU* 3.5 13.9 - - + +
113S PHE* 1.3 75.6 - - - +
115S ALA* 1.3 60.5 + - - +
117S LYS* 2.9 25.8 + - - +
119S VAL* 3.2 45.5 - - + +
121S LEU* 4.0 9.0 - - + -
140S MET* 4.5 14.6 - - + +
143S THR* 4.4 6.5 - - + +
144S ILE* 3.4 34.3 - - + -
148S PHE* 4.6 6.7 - - + -
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Residues in contact with ALA 115 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68H LYS* 5.1 10.1 - - + -
111S LEU 2.9 14.0 + - - +
112S ASP* 3.6 9.4 - - - +
114S ILE* 1.3 75.9 - - - +
116S SER* 1.3 60.9 + - - +
117S LYS 3.1 1.2 + - - -
118S GLY* 3.1 11.6 + - - -
119S VAL 3.2 21.2 + - - +
121S LEU* 3.4 20.4 - - + -
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Residues in contact with SER 116 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112S ASP 2.8 14.3 + - - -
113S PHE* 2.5 31.0 + - - -
115S ALA* 1.3 76.2 - - - +
117S LYS* 1.3 64.2 + - - +
118S GLY 3.1 4.5 + - - -
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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