Contacts of the helix formed by residues 107 - 123 (chain C) in PDB entry 4B94
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 GLU 107 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C GLN 3.6 4.6 + - - -
106C ASN* 1.3 70.4 + - - +
108C SER* 1.3 60.7 + - - +
110C ALA* 3.3 3.6 + - - +
111C ARG* 3.1 35.4 + - + +
142C PHE* 3.7 37.3 - - + -
144C PHE* 4.2 17.9 - - + -
1197C PEG 5.6 0.6 - - - -
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Residues in contact with SER 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C PRO* 3.9 25.8 - - - -
63C GLU* 3.6 21.1 + - - +
66C LEU* 3.9 22.3 - - - +
106C ASN* 3.0 10.5 + - - -
107C GLU* 1.3 72.9 - - - +
109C PHE* 1.3 60.0 + - - +
111C ARG* 3.3 5.5 + - - +
112C ILE* 3.1 31.6 + - - +
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Residues in contact with PHE 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C PRO* 3.6 12.7 - - + +
95C ILE* 5.5 4.7 - - + -
98C LEU* 3.7 40.6 - - + -
100C PRO* 3.8 32.5 - - + -
103C TYR* 3.3 40.2 - + + +
106C ASN* 3.0 13.5 + - - +
107C GLU 3.3 0.2 - - - -
108C SER* 1.3 74.2 - - - +
110C ALA* 1.3 63.1 + - - +
112C ILE* 3.2 8.5 + - + +
113C GLN* 3.0 52.7 + - + +
138C ASN* 4.1 7.4 - - + -
139C CYS* 3.8 23.1 - - - -
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Residues in contact with ALA 110 (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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106C ASN 3.1 8.2 + - - +
107C GLU 3.5 9.4 - - - +
109C PHE* 1.3 76.5 - - - +
111C ARG* 1.3 56.8 + - - +
113C GLN* 3.4 1.4 + - - +
114C VAL* 3.0 34.1 + - - +
139C CYS* 3.6 25.8 - - + -
142C PHE* 3.7 25.4 - - + -
144C PHE* 3.6 17.9 - - + -
145C VAL* 3.9 2.7 - - + -
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Residues in contact with ARG 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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66C LEU* 3.8 32.4 - - + +
70C LEU* 3.7 29.5 - - - +
107C GLU* 3.1 25.5 + - - +
108C SER* 3.3 10.5 + - - +
110C ALA* 1.3 71.5 - - - +
112C ILE* 1.3 58.3 - - - +
114C VAL* 3.9 1.5 - - - +
115C ARG* 2.9 34.2 + - - +
144C PHE* 3.7 23.6 - - + -
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Residues in contact with ILE 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C PRO* 3.5 27.6 - - + +
65C TRP* 3.9 11.9 - - + -
66C LEU* 3.9 17.3 - - + +
69C LEU* 4.1 7.0 - - + -
91C TYR* 3.6 22.5 - - + -
94C ALA* 4.1 11.4 - - + -
95C ILE* 4.0 22.4 - - + +
98C LEU* 3.8 25.6 - - + -
108C SER 3.1 17.0 + - - +
109C PHE* 3.2 9.4 + - + +
111C ARG* 1.3 76.0 - - - +
113C GLN* 1.3 63.3 + - + +
116C PHE* 3.1 23.6 + - - +
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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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92A SER* 5.5 0.2 + - - -
96A GLU* 3.6 21.0 + - - +
95C ILE* 3.9 23.8 - - + +
100C PRO* 5.0 2.2 - - - +
109C PHE* 3.0 53.4 + - + +
110C ALA 3.8 3.6 - - - +
112C ILE* 1.3 74.4 - - + +
114C VAL* 1.3 61.4 + - - +
116C PHE* 3.7 8.0 - - - +
117C ALA* 3.4 21.0 + - - +
131C TYR 4.5 1.6 - - - +
134C MET 3.5 0.5 - - - +
135C ALA* 3.5 31.0 - - + +
138C ASN* 3.0 28.9 + - - +
139C CYS* 4.0 6.3 - - - -
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Residues in contact with VAL 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 ALA 3.0 20.6 + - - +
111C ARG* 4.0 2.9 - - - +
113C GLN* 1.3 74.4 - - - +
115C ARG* 1.4 62.0 + - - +
117C ALA* 3.2 7.3 + - - +
118C GLU* 2.9 38.7 + - - +
132C PHE* 6.1 1.1 - - + -
135C ALA* 4.3 7.6 - - + -
144C PHE* 3.8 16.8 - - + -
145C VAL* 3.7 41.7 - - + +
148C SER* 3.3 27.5 + - - +
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Residues in contact with ARG 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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66C LEU* 6.2 0.7 - - + -
70C LEU* 6.0 3.6 - - + -
73C GLU* 2.7 32.1 + - - +
91C TYR* 3.5 31.6 - - + +
111C ARG 2.9 21.6 + - - +
114C VAL* 1.4 73.3 - - + +
116C PHE* 1.3 53.4 + - - +
118C GLU* 3.2 38.9 + - - +
119C LEU* 2.7 58.5 + - + +
122C ILE* 4.7 11.5 - - - +
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Residues in contact with PHE 116 (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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96A GLU* 3.6 34.1 - - + -
88C ILE* 3.9 12.8 - - + -
91C TYR* 3.7 27.9 - - + -
92C SER* 3.3 28.3 - - - -
95C ILE* 3.5 24.5 - - + -
112C ILE 3.1 18.4 + - - +
113C GLN 3.7 3.8 - - - +
115C ARG* 1.3 76.3 - - - +
117C ALA* 1.4 57.3 + - - +
119C LEU* 3.3 5.4 + - - +
120C LYS* 2.9 60.9 + - + +
131C TYR* 3.6 28.0 - + + -
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Residues in contact with ALA 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C GLN 3.4 6.7 + - - +
114C VAL* 3.2 11.7 + - - +
116C PHE* 1.4 77.5 - - - +
118C GLU* 1.3 57.8 + - - +
120C LYS* 3.4 3.0 + - - +
121C ALA* 3.0 27.7 + - - +
128C ALA* 4.3 0.5 - - - +
131C TYR* 3.7 37.2 - - + +
132C PHE* 3.5 33.0 - - + +
135C ALA* 5.1 0.7 - - + -
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Residues in contact with GLU 118 (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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114C VAL* 2.9 28.2 + - - +
115C ARG* 3.2 38.7 + - - +
117C ALA* 1.3 73.0 - - - +
119C LEU* 1.3 65.3 + - - +
121C ALA* 3.4 4.5 + - - +
122C ILE* 3.2 28.7 + - + +
132C PHE* 4.1 11.2 - - + -
148C SER* 2.6 30.9 + - - +
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Residues in contact with LEU 119 (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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73C GLU* 4.7 0.2 - - - +
79C LEU* 6.0 1.8 - - + -
84C LEU* 3.8 21.1 - - + +
87C LEU* 4.0 22.2 - - + -
88C ILE* 3.7 24.5 - - + +
91C TYR* 3.7 38.1 - - + -
115C ARG* 2.7 53.3 + - + +
116C PHE* 3.3 4.2 + - - +
118C GLU* 1.3 73.0 - - - +
120C LYS* 1.3 63.1 + - - +
122C ILE* 3.2 14.9 + - + +
123C GLN* 3.1 22.0 + - - +
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Residues in contact with LYS 120 (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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96A GLU 5.2 0.9 - - - -
99A PRO* 4.8 11.3 - - - +
88C ILE* 3.8 19.9 - - + +
92C SER* 5.3 1.8 + - - -
116C PHE* 2.9 50.0 + - + +
117C ALA 3.6 4.3 - - - +
119C LEU* 1.3 75.9 - - - +
121C ALA* 1.4 49.9 + - - +
123C GLN* 3.2 26.4 + - - +
124C GLU* 2.8 36.2 + - - +
128C ALA* 3.9 4.9 - - + -
131C TYR* 3.6 49.6 + - + -
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Residues in contact with ALA 121 (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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117C ALA 3.0 17.5 + - - +
118C GLU* 3.6 7.0 - - - +
120C LYS* 1.4 72.4 - - - +
122C ILE* 1.4 64.6 + - + +
125C PRO* 3.1 29.8 - - + +
128C ALA* 3.6 10.9 - - + +
132C PHE* 4.0 19.1 - - + -
152C PHE* 4.0 16.8 - - + -
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Residues in contact with ILE 122 (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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79C LEU* 5.5 8.3 - - + -
84C LEU* 4.0 18.6 - - + -
115C ARG* 4.7 12.1 - - - +
118C GLU* 3.2 18.3 + - + +
119C LEU* 3.2 26.7 + - + +
121C ALA* 1.4 76.0 - - + +
123C GLN* 1.4 64.4 - - - +
124C GLU 3.6 0.2 + - - -
125C PRO* 4.3 4.2 - - - +
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Residues in contact with GLN 123 (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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81C ASP 5.7 0.2 + - - -
84C LEU* 4.1 15.0 - - + +
85C ASN* 2.8 36.4 + - - +
88C ILE* 3.6 25.2 - - + +
119C LEU 3.1 12.6 + - - +
120C LYS* 3.4 29.3 + - - +
122C ILE* 1.4 79.1 - - - +
124C GLU* 1.4 66.7 + - + +
125C PRO* 4.6 0.5 - - - +
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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
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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