Contacts of the helix formed by residues 108 - 123 (chain F) in PDB entry 3D29
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 PRO 108 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99F PHE* 3.5 22.9 - - + -
105F THR* 5.2 4.3 - - + +
106F PRO 3.6 5.8 - - - +
107F ILE* 1.3 93.0 - - + +
109F ILE* 1.3 67.3 + - - +
110F PRO* 4.1 7.4 - - + -
111F ALA* 3.0 13.9 + - + +
112F PHE* 2.9 18.7 + - - +
142F ASP* 3.6 20.6 - - + +
143F LYS* 6.4 2.5 - - + -
144F ASN* 5.8 1.6 - - - +
66N TYR* 4.9 7.6 - - - +
70N TYR* 5.4 7.0 - - + +
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Residues in contact with ILE 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73F HIS* 3.8 14.6 - - + -
74F ILE* 3.7 22.4 - - + -
108F PRO* 1.3 69.9 - - - +
110F PRO* 1.3 66.1 - - + +
112F PHE* 3.1 8.3 + - + +
113F ALA* 2.9 27.7 + - - +
138F PHE* 4.9 4.9 - - + -
139F GLY* 3.7 24.7 - - - -
140F GLY* 3.5 38.1 - - - +
141F VAL 4.0 2.0 - - - +
142F ASP* 3.1 7.2 + - + +
147F HIS* 3.7 26.0 - - + +
149F TYR* 3.9 9.9 - - + -
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Residues in contact with PRO 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108F PRO* 3.4 7.9 - - + -
109F ILE* 1.3 93.8 - - + +
111F ALA* 1.3 60.7 + - - +
113F ALA* 3.3 3.8 + - - +
114F ASP* 3.3 20.3 + - - +
142F ASP* 3.3 14.1 - - - +
147F HIS* 3.8 18.6 - - + +
149F TYR* 3.5 25.8 - - + +
157F TYR* 4.8 1.7 + - - -
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Residues in contact with ALA 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99F PHE* 4.4 1.3 - - + -
107F ILE* 3.9 16.6 - - + -
108F PRO* 3.0 19.7 + - + +
110F PRO* 1.3 77.2 - - - +
112F PHE* 1.3 66.4 + - - +
114F ASP* 3.4 5.7 + - - +
115F ARG* 3.1 25.3 + - - +
70N TYR* 3.2 43.7 - - + -
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Residues in contact with PHE 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70F VAL* 3.7 27.6 - - + -
74F ILE* 3.7 35.9 - - + -
76F CYS* 4.3 4.0 - - - -
89F VAL* 6.3 0.2 - - - -
92F GLY* 3.7 31.9 - - - -
95F GLU* 5.2 0.7 - - + -
96F ALA* 4.8 1.3 - - + -
107F ILE* 3.7 23.0 - - + +
108F PRO 2.9 11.6 + - - +
109F ILE* 3.4 8.5 - - + +
111F ALA* 1.3 79.7 - - - +
113F ALA* 1.3 63.1 + - - +
115F ARG* 3.0 17.1 + - + +
116F LEU* 3.0 46.1 + - + +
138F PHE* 3.7 27.8 - + - -
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Residues in contact with ALA 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109F ILE 2.9 13.3 + - - +
110F PRO 3.5 9.2 - - - +
112F PHE* 1.3 77.0 - - - +
114F ASP* 1.3 57.4 + - - +
116F LEU* 3.2 5.5 + - - +
117F GLY* 2.8 24.8 + - - -
138F PHE* 3.7 30.7 - - + -
149F TYR* 4.0 15.3 - - + -
151F LEU* 5.2 0.2 - - - +
157F TYR* 3.8 24.4 - - + -
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Residues in contact with ASP 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110F PRO 3.3 9.0 + - - +
111F ALA* 4.0 8.1 - - - +
112F PHE 3.3 0.2 - - - -
113F ALA* 1.3 76.5 - - - +
115F ARG* 1.3 66.5 + - - +
117F GLY 3.6 0.4 - - - -
118F GLN* 2.9 62.8 + - - +
157F TYR* 2.9 30.9 + - - +
86G ARG* 4.1 10.4 - - - +
90G LEU* 4.7 8.1 - - - +
69N GLN* 5.1 3.6 - - - +
70N TYR* 6.0 4.2 - - + -
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Residues in contact with ARG 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F ARG* 5.8 0.4 - - - +
95F GLU* 2.9 73.6 + - + +
98F SER* 4.2 10.5 + - - -
99F PHE* 3.8 22.9 - - - +
103F TYR* 4.8 6.7 + - - -
107F ILE* 4.2 8.5 - - + +
111F ALA 3.1 17.8 + - - +
112F PHE* 3.0 13.5 + - + +
114F ASP* 1.3 79.4 - - - +
116F LEU* 1.3 63.1 + - + +
118F GLN* 4.2 5.2 - - - +
119F TYR* 3.4 20.1 + - - +
69N GLN* 5.0 2.8 + - - -
70N TYR* 2.9 29.7 + - + -
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Residues in contact with LEU 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76F CYS* 5.2 4.0 - - - -
88F LEU* 4.1 29.4 - - + +
89F VAL* 5.8 0.2 - - - -
91F ARG* 5.1 2.7 - - + -
92F GLY* 3.8 20.4 - - - +
95F GLU* 5.7 0.7 - - + -
112F PHE* 3.0 53.4 + - + +
113F ALA 3.6 4.9 - - - +
115F ARG* 1.3 77.2 - - + +
117F GLY* 1.3 58.0 - - - +
119F TYR* 3.3 6.4 + - - +
120F VAL* 2.9 33.6 + - - +
136F THR* 5.4 2.7 - - + -
138F PHE* 3.9 25.8 - - + -
151F LEU* 3.6 16.8 - - + -
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Residues in contact with GLY 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F ALA 2.8 14.0 + - - -
114F ASP* 3.3 3.3 + - - -
115F ARG 3.2 0.2 - - - -
116F LEU* 1.3 78.1 - - - +
118F GLN* 1.3 56.3 + - - +
120F VAL* 3.3 2.3 + - - +
121F GLN* 2.8 31.5 + - - +
151F LEU* 3.9 20.4 - - - +
155F GLY 4.1 5.7 - - - +
157F TYR* 4.0 13.0 - - - -
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Residues in contact with GLN 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F ASP* 2.9 51.6 + - - +
115F ARG* 4.2 5.6 - - - +
117F GLY* 1.3 71.9 - - - -
119F TYR* 1.3 57.4 + - - +
121F GLN* 3.4 10.2 + - - +
122F ALA* 2.8 29.5 + - - +
83G PRO 5.0 0.9 - - - +
86G ARG* 3.3 27.6 + - - +
87G ASN* 3.5 23.3 + - - +
90G LEU* 3.6 30.2 - - + +
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Residues in contact with TYR 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87F HIS* 3.2 30.0 + - - -
88F LEU* 3.6 21.1 - - + -
91F ARG* 3.5 68.6 + - + +
95F GLU* 5.3 0.2 - - - +
115F ARG 3.4 11.7 + - - +
116F LEU* 3.3 8.2 + - - +
117F GLY 3.2 0.2 - - - -
118F GLN* 1.3 76.6 - - - +
120F VAL* 1.3 61.8 + - - +
122F ALA* 3.1 14.6 + - + +
123F HIS* 2.9 41.9 + + - -
132F PHE* 3.5 22.0 - + - -
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Residues in contact with VAL 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88F LEU* 3.7 24.7 - - + -
116F LEU 2.9 20.5 + - - +
117F GLY 3.9 3.1 - - - +
119F TYR* 1.3 76.7 - - - +
121F GLN* 1.3 63.8 + - - +
123F HIS* 3.1 17.2 + - - +
124F THR* 3.7 7.6 - - - +
132F PHE* 4.1 24.7 - - + -
151F LEU* 3.7 19.5 - - + -
152F GLU 3.5 24.9 - - - +
153F PRO* 3.6 14.0 - - + +
155F GLY* 3.6 10.3 - - - -
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Residues in contact with GLN 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117F GLY 2.8 18.6 + - - +
118F GLN* 3.6 11.2 + - - +
120F VAL* 1.3 77.5 - - - +
122F ALA* 1.3 71.0 + - - +
124F THR* 2.7 28.1 + - - +
125F LEU* 3.7 18.8 - - - +
154F SER 4.0 10.5 - - - +
155F GLY* 4.1 0.6 - - - -
83G PRO* 3.6 36.6 - - + +
84G ASP* 3.0 23.3 - - - +
87G ASN* 3.3 37.1 + - + +
130G ARG* 3.9 0.5 + - - -
132G LEU* 4.1 0.2 - - - +
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Residues in contact with ALA 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118F GLN 2.8 14.3 + - - +
119F TYR* 3.2 17.3 - - + +
121F GLN* 1.3 84.7 - - - +
123F HIS* 1.3 60.3 + - + +
124F THR 3.1 4.7 + - - -
125F LEU* 3.3 26.7 + - + +
126F TYR* 3.6 18.3 - - + -
129F VAL* 4.6 0.3 - - - +
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Residues in contact with HIS 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125E GLN* 3.4 28.4 + - + -
12F ASN* 2.9 20.9 + - - -
87F HIS* 4.8 2.4 + - - -
119F TYR* 2.9 49.6 + + - -
120F VAL 3.1 8.7 + - - +
121F GLN 3.1 1.4 - - - -
122F ALA* 1.3 79.8 - - + +
124F THR* 1.3 59.5 + - - +
125F LEU 3.5 0.9 - - - -
129F VAL* 3.9 27.6 - - + +
130F ARG 3.7 12.3 - - - +
131F PRO* 3.5 13.4 - - + +
132F PHE* 3.5 25.7 - + + -
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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