Contacts of the helix formed by residues 94 - 116 (chain C) in PDB entry 4LLL
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 THR 94 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C LYS 2.6 26.0 + - - +
76C LEU 3.0 13.8 + - - -
77C ILE 3.4 25.1 - - - +
78C TYR* 4.0 15.9 - - + -
92C GLY 3.7 0.8 + - - -
93C LEU* 1.3 73.9 - - - +
95C THR* 1.3 52.4 + - - +
96C SER* 3.0 9.6 + - - -
97C GLY 2.7 23.4 + - - -
98C ILE* 2.7 17.3 + - - -
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Residues in contact with THR 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C LEU 4.0 0.4 + - - -
94C THR* 1.3 71.1 - - - +
96C SER* 1.3 59.0 + - - +
98C ILE* 3.0 21.3 + - + +
99C LYS* 2.8 31.6 + - + +
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Residues in contact with SER 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C LYS 5.2 0.2 + - - -
75C LYS* 3.1 13.2 + - - +
76C LEU* 4.0 11.8 - - - +
94C THR* 3.0 14.1 + - - -
95C THR* 1.3 78.4 - - - +
97C GLY* 1.3 59.4 + - - +
99C LYS* 3.1 7.4 + - - +
100C LEU* 2.8 34.8 + - - +
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Residues in contact with GLY 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C LEU* 5.5 1.1 - - - +
76C LEU* 3.5 31.2 - - - -
93C LEU* 4.4 10.5 - - - -
94C THR* 2.7 14.4 + - - -
96C SER* 1.3 78.6 + - - +
98C ILE* 1.3 61.2 + - - -
100C LEU* 3.0 5.3 + - - +
101C VAL* 2.9 26.2 + - - +
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Residues in contact with ILE 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C TYR* 3.6 25.7 - - + -
44C GLN* 5.1 8.1 - - - +
93C LEU* 4.0 26.6 - - + +
94C THR 2.7 22.3 + - - +
95C THR* 3.4 23.3 - - + +
97C GLY* 1.3 70.3 - - - +
99C LYS* 1.3 63.4 + - - +
101C VAL* 3.6 0.7 + - - +
102C GLU* 3.3 31.3 + - - +
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Residues in contact with LYS 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C THR* 2.8 15.5 + - + +
96C SER* 3.6 9.0 - - - +
98C ILE* 1.3 73.6 - - - +
100C LEU* 1.3 67.2 + - - +
102C GLU* 2.9 24.9 + - - +
103C ALA* 2.9 13.4 + - - +
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Residues in contact with LEU 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C PHE* 3.5 45.3 - - + +
29C ILE* 3.8 18.6 - - + -
37C LEU* 3.9 11.4 - - + -
76C LEU* 3.6 37.9 - - + -
96C SER 2.8 13.1 + - - +
97C GLY* 3.3 10.3 - - - +
99C LYS* 1.3 76.0 - - - +
101C VAL* 1.3 62.4 + - - +
103C ALA* 3.1 7.6 + - + +
104C PHE* 3.0 33.7 + - + -
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Residues in contact with VAL 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C LEU* 3.6 41.5 - - + +
38C GLY* 4.6 7.0 - - - -
41C TYR* 3.7 41.1 - - + -
93C LEU* 4.3 4.3 - - + -
97C GLY 2.9 15.8 + - - +
98C ILE 4.0 0.2 - - - +
100C LEU* 1.3 74.4 - - - +
102C GLU* 1.3 65.0 + - - +
104C PHE* 3.6 17.0 - - + -
105C THR* 3.0 40.5 + - - +
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Residues in contact with GLU 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C TYR* 3.3 33.8 + - + +
98C ILE* 3.3 23.7 + - - +
99C LYS* 2.9 14.7 + - - +
101C VAL* 1.3 77.9 - - - +
103C ALA* 1.3 62.5 + - - +
105C THR* 3.7 15.1 - - - +
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Residues in contact with ALA 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C PHE* 3.4 26.8 - - + -
99C LYS 2.9 10.2 + - - +
100C LEU* 3.3 12.3 - - + +
101C VAL 3.0 1.0 - - - -
102C GLU* 1.3 80.5 - - - +
104C PHE* 1.3 60.8 + - - +
105C THR 3.2 2.8 + - - -
106C SER* 3.7 13.0 + - - -
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Residues in contact with PHE 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C LEU* 3.5 24.2 - - + -
27C PHE* 3.8 20.2 - - + -
29C ILE* 3.5 24.2 - - + -
34C GLY* 3.2 22.2 - - - -
37C LEU* 4.1 6.1 - - + -
38C GLY* 4.5 2.5 - - - -
100C LEU* 3.0 29.6 + - + +
101C VAL* 3.6 36.6 - - + -
103C ALA* 1.3 74.8 - - - +
105C THR* 1.3 73.0 + - - +
106C SER 3.1 2.9 - - - -
107C ILE* 2.9 24.6 + - - +
108C PHE* 3.5 33.0 + + - -
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Residues in contact with THR 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C VAL* 3.0 30.5 + - - +
102C GLU* 3.7 17.0 - - - +
103C ALA 3.2 0.4 - - - -
104C PHE* 1.3 86.3 - - - +
106C SER* 1.3 70.6 + - - +
108C PHE* 3.3 18.4 + - - +
109C ASP* 3.4 19.4 + - - +
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Residues in contact with SER 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C ALA 3.7 13.6 + - - -
104C PHE 4.3 0.3 - - - -
105C THR* 1.3 86.4 - - - +
107C ILE* 1.3 54.2 + - - +
109C ASP* 2.6 21.1 + - - +
110C GLU* 2.4 53.2 + - - +
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Residues in contact with ILE 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ALA* 4.9 5.4 - - - +
23C LYS* 3.6 49.6 - - + +
24C LEU* 3.8 28.5 - - + -
26C GLN* 4.6 3.6 - - - +
27C PHE* 3.8 20.4 - - + -
104C PHE* 2.9 15.4 + - - +
106C SER* 1.3 83.8 + - - +
108C PHE* 1.3 67.7 + - + +
110C GLU* 3.2 18.3 + - - +
111C MET* 3.2 26.7 + - + +
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Residues in contact with PHE 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ALA* 4.2 7.0 - - + -
24C LEU* 4.0 20.0 - - + -
31C ASN* 3.9 16.6 - - - -
34C GLY* 3.6 22.7 - - - -
35C HIS* 3.4 41.3 - + + -
38C GLY* 5.9 1.3 - - - -
104C PHE* 3.5 33.2 + + - -
105C THR* 3.3 10.0 + - - +
106C SER 3.2 0.6 - - - -
107C ILE* 1.3 79.1 - - + +
109C ASP* 1.3 64.8 + - - +
111C MET* 3.3 21.2 + - + +
112C GLU* 3.0 25.0 + - - +
4D THR* 5.7 2.6 - - + +
6D SER* 6.1 3.6 - - - -
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Residues in contact with ASP 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C THR* 3.4 19.0 + - - +
106C SER* 2.6 25.6 + - - +
108C PHE* 1.3 74.4 - - - +
110C GLU* 1.3 53.9 + - + +
111C MET 2.9 1.4 + - - -
112C GLU* 3.1 5.4 + - - +
113C GLN* 2.9 37.3 + - + +
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Residues in contact with GLU 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C LYS* 4.5 17.1 + - - +
106C SER* 2.4 38.5 + - - +
107C ILE* 3.2 32.9 + - - +
109C ASP* 1.3 66.5 - - + +
111C MET* 1.3 52.0 + - - +
113C GLN* 5.4 2.0 - - - -
114C THR* 2.2 31.0 + - - -
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Residues in contact with MET 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C MET* 3.7 46.0 - - + +
19C LYS* 4.2 10.3 - - - -
20C ALA* 4.2 23.6 - - + -
23C LYS* 4.0 16.8 - - - +
31C ASN* 5.7 0.7 - - - +
35C HIS* 5.9 0.2 - - + -
107C ILE* 3.2 14.6 + - + +
108C PHE* 3.7 28.9 - - + +
109C ASP 3.0 0.6 - - - -
110C GLU* 1.3 79.0 - - - +
112C GLU* 1.3 54.6 - - - +
113C GLN 3.3 1.1 - - - -
114C THR* 3.1 7.8 + - - -
115C LEU* 2.8 39.3 + - + +
6D SER* 5.1 6.7 - - - +
138D LEU* 5.8 5.6 - - + -
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Residues in contact with GLU 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C MET* 5.8 1.5 - - - +
108C PHE 3.0 17.2 + - - +
109C ASP* 3.8 7.0 - - - +
111C MET* 1.3 78.7 - - - +
113C GLN* 1.3 56.8 + - + +
115C LEU* 3.3 5.0 + - - +
116C VAL* 3.0 53.7 + - + +
3D PHE 4.6 1.4 - - - +
4D THR* 3.1 25.2 - - + +
5D TYR* 2.9 45.0 + - - +
6D SER* 3.6 3.3 + - - -
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Residues in contact with GLN 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C ASP* 2.9 16.2 + - + +
110C GLU* 5.4 2.0 - - - -
112C GLU* 1.3 75.7 - - - +
114C THR* 1.3 62.5 + - - +
115C LEU 3.4 0.2 - - - -
116C VAL* 3.7 14.7 - - + +
117C SER* 3.5 19.9 + - - -
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Residues in contact with THR 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C GLU 2.2 28.7 + - - -
111C MET* 3.1 12.2 + - - -
113C GLN* 1.3 77.5 - - - +
115C LEU* 1.3 62.5 + - + +
117C SER* 2.6 24.0 + - - +
118C GLN* 3.3 11.4 + - - +
137D SER* 5.1 12.1 - - - +
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Residues in contact with LEU 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C MET* 4.2 27.4 - - + -
111C MET* 2.8 19.0 + - + +
112C GLU* 3.6 7.4 - - - +
114C THR* 1.3 75.9 - - + +
116C VAL* 1.3 58.2 - - - +
117C SER 2.9 5.4 + - - -
118C GLN* 2.5 24.7 + - - +
119C LEU* 4.5 1.7 + - - +
5D TYR* 3.6 44.2 - - + -
9D PHE* 4.3 9.4 - - + -
134D MET* 4.1 38.8 - - + +
137D SER* 4.6 5.8 - - - +
138D LEU* 4.5 19.7 - - + -
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Residues in contact with VAL 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C GLU* 3.0 36.4 + - + +
113C GLN* 3.7 20.0 - - + +
115C LEU* 1.3 74.8 - - - +
117C SER* 1.3 58.8 + - - +
118C GLN 3.5 0.4 - - - -
119C LEU* 2.8 35.3 + - - +
124C ASN* 5.6 4.0 - - + -
5D TYR* 4.2 22.4 - - + +
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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