Contacts of the helix formed by residues 103 - 118 (chain F) in PDB entry 4GOO
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 ASP 103 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101F SER* 3.3 11.6 + - - +
102F GLN* 1.3 76.0 - - - +
104F PRO* 1.3 72.0 - - - +
105F PHE* 2.7 23.2 + - - +
106F ARG* 3.5 19.6 + - + +
107F ARG* 3.1 21.6 + - - +
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Residues in contact with PRO 104 (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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61F SER* 4.3 17.8 + - - +
65F ILE* 3.7 9.0 - - + +
102F GLN 3.4 11.0 - - - +
103F ASP* 1.3 85.3 - - - +
105F PHE* 1.3 62.4 + - - +
107F ARG* 3.5 9.9 + - + +
108F ALA* 3.1 23.9 + - - +
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Residues in contact with PHE 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65F ILE* 3.9 28.5 - - + -
69F ARG* 3.7 34.8 - - + +
72F GLU* 3.7 43.7 - - + -
73F TYR* 3.9 24.2 - + + -
76F ALA* 4.1 13.7 - - + -
103F ASP* 2.7 18.9 + - - +
104F PRO* 1.3 71.0 - - + +
106F ARG* 1.3 68.0 + - + +
108F ALA* 3.0 12.5 + - - +
109F VAL* 3.1 29.6 + - + +
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Residues in contact with ARG 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80F LEU* 4.3 22.6 - - - +
94F PHE* 4.7 9.1 - - - -
97F GLU* 2.5 41.8 + - - +
101F SER* 4.2 10.5 - - - +
103F ASP* 3.3 25.8 + - + +
105F PHE* 1.3 82.9 - - + +
107F ARG* 1.3 61.7 + - - +
109F VAL* 3.2 12.8 + - - +
110F LEU* 3.1 49.2 + - + +
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Residues in contact with ARG 107 (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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58F ASP* 2.7 31.9 + - - -
98F PHE* 2.8 76.1 + - + +
99F ASN* 4.4 6.1 + - - +
101F SER* 3.4 36.8 + - - -
102F GLN* 4.8 1.8 - - - +
103F ASP 3.1 22.3 + - - +
104F PRO* 3.5 9.2 - - + +
106F ARG* 1.3 77.6 - - - +
108F ALA* 1.3 56.0 + - - +
110F LEU* 4.6 2.5 - - - -
111F PHE* 2.9 22.3 + - - +
125F TYR* 5.8 0.8 - - - -
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Residues in contact with ALA 108 (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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58F ASP 5.8 0.2 - - - +
61F SER* 5.6 0.4 - - - +
62F LEU* 4.1 25.9 - - + +
65F ILE* 4.0 17.9 - - + -
73F TYR* 3.1 27.2 + - + -
104F PRO 3.1 14.2 + - - +
105F PHE 3.0 6.6 + - - +
107F ARG* 1.3 75.5 - - - +
109F VAL* 1.3 66.7 + - - +
111F PHE* 3.7 9.3 - - - +
112F LEU 3.6 8.8 + - - -
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Residues in contact with VAL 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73F TYR* 3.9 24.5 - - + -
76F ALA* 3.8 28.0 - - + +
77F ALA* 3.7 29.8 - - - +
80F LEU* 4.3 19.1 - - + +
81F PHE* 5.8 0.5 - - - -
105F PHE* 3.1 24.9 + - + +
106F ARG* 3.2 16.4 + - - +
108F ALA* 1.3 78.1 - - - +
110F LEU* 1.3 62.7 + - - +
112F LEU* 3.0 16.3 + - - +
113F TYR* 3.4 8.8 + - - +
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Residues in contact with LEU 110 (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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80F LEU* 3.9 22.0 - - + -
94F PHE* 4.0 31.9 - - + +
97F GLU* 4.0 20.9 - - + +
98F PHE* 3.9 39.7 - - + +
101F SER* 5.4 0.2 - - - -
106F ARG* 3.1 41.4 + - + +
107F ARG* 3.8 5.4 - - - +
109F VAL* 1.3 73.0 - - - +
111F PHE* 1.3 68.0 + - - +
113F TYR* 2.8 18.8 + - + +
114F LEU* 2.9 17.9 + - + +
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Residues in contact with PHE 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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8F LEU* 4.5 12.1 - - + -
56F ASN* 4.9 1.8 - - - -
58F ASP* 3.6 30.7 - - + -
59F LEU* 4.1 17.9 - - + -
62F LEU* 3.7 31.0 - - + -
98F PHE* 4.0 18.3 - + + -
107F ARG 2.9 19.0 + - - +
108F ALA* 3.7 11.2 - - - +
109F VAL 3.3 0.2 - - - -
110F LEU* 1.3 76.1 - - - +
112F LEU* 1.3 57.2 + - - +
114F LEU* 3.5 9.5 + - + +
115F ASN* 3.1 27.6 + - + +
123F CYS* 3.9 30.3 - - - -
125F TYR* 4.2 3.6 - - - -
131F PHE* 5.1 8.7 - + - -
301F 0Y2 4.4 10.5 - + - -
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Residues in contact with LEU 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F PHE* 4.0 24.0 - - + +
8F LEU* 3.9 24.0 - - + -
62F LEU* 5.5 2.2 - - + -
73F TYR* 3.4 27.4 - - - +
77F ALA* 4.2 6.3 - - + -
81F PHE* 4.0 11.2 - - + -
108F ALA 3.6 1.6 + - - +
109F VAL 3.0 6.0 + - - +
110F LEU 3.0 1.2 - - - -
111F PHE* 1.3 78.1 - - - +
113F TYR* 1.3 69.6 + - - +
115F ASN* 3.3 3.2 + - - +
116F ARG* 3.2 29.6 + - + +
143F PHE* 3.8 29.2 - - + -
144F PRO* 4.6 4.5 - - + -
148F LEU* 4.1 15.3 - - + -
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Residues in contact with TYR 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80F LEU* 4.0 31.2 - - + -
81F PHE* 4.1 12.0 - + + -
85F THR* 3.0 29.9 + - - -
87F CYS 4.9 0.3 + - - -
90F VAL* 4.1 0.5 - - - +
91F TYR* 3.5 46.2 + + - +
94F PHE* 3.7 33.2 - + + -
109F VAL 3.4 3.0 + - - +
110F LEU* 2.8 9.5 + - - +
112F LEU* 1.3 78.4 - - - +
114F LEU* 1.3 69.1 + - + +
116F ARG 3.0 2.6 + - - -
117F TYR* 2.9 77.3 + + + +
135F PHE* 5.0 0.3 - - - -
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Residues in contact with LEU 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91F TYR* 3.8 22.9 + - + -
94F PHE* 4.7 1.3 - - + -
95F ARG* 4.1 23.3 - - + +
98F PHE* 3.9 36.3 - - + -
110F LEU* 2.9 16.2 + - + +
111F PHE* 3.6 10.8 - - + +
113F TYR* 1.3 97.5 - - + +
115F ASN* 1.3 60.9 + - - +
118F GLY* 3.3 21.1 + - - -
121F GLY* 5.6 0.5 - - - -
122F LEU 5.3 1.4 + - - +
131F PHE* 3.4 46.7 - - + -
133F VAL* 5.7 0.3 - - - +
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Residues in contact with ASN 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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8F LEU* 3.5 27.4 - - + +
9F LYS* 3.0 51.3 + - - +
111F PHE* 3.1 22.7 + - + +
112F LEU 3.3 2.6 + - - +
113F TYR 3.1 0.6 - - - -
114F LEU* 1.3 77.8 - - - +
116F ARG* 1.3 69.1 + - - +
117F TYR 3.5 0.2 - - - -
118F GLY 4.3 1.9 + - - +
121F GLY* 3.4 37.4 + - - -
122F LEU 5.5 3.8 + - - +
131F PHE* 5.7 0.9 - - - -
301F 0Y2 4.5 8.3 - - - -
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Residues in contact with ARG 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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6F ALA 4.1 6.9 + - - -
7F PHE 3.0 33.1 + - - -
8F LEU 4.4 0.8 - - - +
9F LYS* 3.9 38.2 - - - +
81F PHE* 3.7 27.1 - - + -
112F LEU* 3.2 22.0 + - + +
113F TYR 3.0 1.8 + - - +
115F ASN* 1.3 86.9 + - - +
117F TYR* 1.3 62.7 + - + +
118F GLY 3.6 0.2 - - - -
138F TYR* 3.8 15.3 - - - -
141F PRO* 3.6 17.8 - - + +
142F TYR* 4.0 36.4 - - - +
144F PRO* 3.8 20.4 - - + +
147F GLU* 5.8 0.2 - - - -
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Residues in contact with TYR 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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80F LEU 4.0 0.4 - - - -
81F PHE* 3.3 50.7 + + - +
82F VAL 3.7 2.9 + - - -
85F THR* 3.3 26.0 + - - -
86F ASN* 3.8 29.5 - - + +
91F TYR* 3.6 5.8 - - + -
113F TYR* 2.9 61.9 + + + +
116F ARG* 1.3 86.3 - - + +
118F GLY* 1.3 56.3 + - - +
135F PHE* 3.2 16.7 - + + -
136F GLY* 3.2 16.3 + - - -
138F TYR* 4.3 8.8 - - - -
141F PRO* 3.6 27.8 + - + +
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Residues in contact with GLY 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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91F TYR* 3.7 9.9 - - - -
114F LEU 3.3 17.8 + - - -
115F ASN 4.3 0.9 + - - +
116F ARG 3.6 1.2 - - - -
117F TYR* 1.3 80.6 - - - +
119F TYR* 1.3 66.1 + - - -
120F ASN 2.9 5.2 + - - -
121F GLY* 3.1 12.7 + - - -
122F LEU 5.1 0.2 - - - -
133F VAL* 4.3 3.4 - - - -
134F PRO 3.6 10.1 - - - -
136F GLY* 3.7 5.2 - - - -
138F TYR* 3.4 8.1 - - - -
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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