Contacts of the helix formed by residues 151 - 167 (chain F) in PDB entry 3GFT
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 GLY 151 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147E LYS 4.8 3.6 + - - -
142F ILE* 4.1 5.2 - - - +
143F GLU 3.9 13.2 - - - -
144F THR* 3.4 5.7 - - - +
149F ARG 3.2 2.0 + - - -
150F GLN* 1.3 73.0 - - - +
152F VAL* 1.3 58.2 + - - +
153F ASP 3.5 1.8 - - - -
154F ASP* 3.5 17.4 - - - +
155F ALA* 2.8 32.9 + - - +
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Residues in contact with VAL 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F LEU* 3.8 40.6 - - + +
22F GLN* 4.2 7.6 - - + -
23F LEU* 4.2 22.2 - - + +
144F THR* 4.7 3.6 - - - -
145F SER 3.4 26.5 - - - +
146F ALA* 4.2 4.5 - - - -
149F ARG* 3.3 23.8 + - + +
150F GLN 3.2 2.0 - - - +
151F GLY* 1.3 76.4 - - - +
153F ASP* 1.3 71.2 + - - +
155F ALA* 3.5 1.8 + - - +
156F PHE* 3.0 32.9 + - + -
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Residues in contact with ASP 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E ASN* 3.8 25.4 + - - +
23F LEU* 3.1 27.7 - - - +
42F LYS* 4.6 2.7 + - - -
149F ARG* 3.1 31.1 + - - -
152F VAL* 1.3 76.5 - - - +
154F ASP* 1.3 56.6 + - - +
156F PHE* 3.1 1.7 + - - -
157F TYR* 2.7 64.8 + - + -
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Residues in contact with ASP 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E GLN* 5.2 0.3 + - - -
26E ASN* 3.1 24.4 + - - +
27E HIS* 2.9 25.0 + - - +
28E PHE* 3.1 28.1 + - - +
142F ILE* 4.1 17.5 - - + +
151F GLY* 3.5 19.2 - - - +
153F ASP* 1.3 79.8 - - - +
155F ALA* 1.3 56.9 + - - +
157F TYR* 4.5 4.0 - - - -
158F THR* 2.8 43.2 + - - -
161F ARG* 4.2 2.3 + - - -
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Residues in contact with ALA 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F LEU* 6.2 1.8 - - + -
79F LEU* 3.6 22.6 - - + +
112F VAL* 4.4 2.5 - - - +
114F VAL* 4.3 18.8 - - + -
142F ILE* 4.3 14.1 - - + -
144F THR* 4.0 16.2 - - + -
151F GLY 2.8 19.3 + - - +
152F VAL* 3.7 5.8 - - - +
153F ASP 3.2 0.2 - - - -
154F ASP* 1.3 75.7 - - - +
156F PHE* 1.3 59.8 + - + +
158F THR* 3.9 1.7 - - - -
159F LEU 3.1 20.6 + - - -
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Residues in contact with PHE 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F LEU* 4.0 22.0 - - + +
8F VAL* 4.3 5.4 - - + -
19F LEU* 4.1 23.8 - - + -
20F THR* 4.3 21.8 - - - -
23F LEU* 3.7 38.6 - - + -
46F ILE* 5.2 0.2 - - - -
53F LEU* 4.7 6.5 - - + -
55F ILE* 4.1 21.3 - - + -
79F LEU* 3.7 28.5 - - + -
152F VAL* 3.0 25.5 + - + -
153F ASP 3.1 5.9 + - - +
155F ALA* 1.3 78.6 - - + +
157F TYR* 1.3 72.2 + - + +
159F LEU* 3.4 7.0 + - - +
160F VAL* 3.1 26.6 + - - +
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Residues in contact with TYR 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E GLN 4.2 6.1 - - - -
26E ASN* 4.2 31.4 + - + -
23F LEU* 4.9 5.8 - - + -
42F LYS* 5.0 3.6 + - - -
44F VAL* 4.0 28.6 - - + +
45F VAL 4.3 9.6 + - - -
46F ILE* 3.8 42.3 - - + +
53F LEU* 5.2 1.6 - - + -
153F ASP* 2.7 53.9 + - + +
154F ASP* 4.1 2.5 - - - +
156F PHE* 1.3 74.2 - - + +
158F THR* 1.3 59.9 + - - +
160F VAL* 3.2 5.9 + - - +
161F ARG* 3.0 44.2 + - - +
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Residues in contact with THR 158 (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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27E HIS* 3.7 12.4 + - + -
112F VAL* 3.9 9.2 - - + -
140F PRO* 3.8 33.9 - - + -
142F ILE* 4.3 6.4 - - + +
154F ASP* 2.8 37.9 + - - -
155F ALA* 3.9 4.5 - - - -
157F TYR* 1.3 74.3 - - - +
159F LEU* 1.3 65.8 + - - +
161F ARG* 3.1 19.7 + - + +
162F GLU* 2.9 22.9 + - + +
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Residues in contact with LEU 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F LEU* 3.9 30.1 - - + -
77F GLY* 3.7 13.5 - - - +
78F PHE 3.6 44.6 - - - +
79F LEU* 3.9 15.7 - - + +
110F PRO* 3.8 2.5 - - + -
111F MET* 3.8 26.5 - - - +
112F VAL* 3.7 9.6 - - + +
155F ALA 3.1 16.1 + - - +
156F PHE* 3.6 8.7 - - - +
157F TYR 3.3 0.2 - - - -
158F THR* 1.3 77.2 - - - +
160F VAL* 1.3 55.8 + - - +
162F GLU* 3.1 5.2 + - + +
163F ILE* 2.9 32.7 + - + +
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Residues in contact with VAL 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F TYR* 3.8 26.5 - - + -
6F LEU* 4.4 7.2 - - + -
46F ILE* 3.8 20.4 - - + -
53F LEU* 3.5 32.3 - - + -
156F PHE 3.1 16.5 + - - +
157F TYR 3.2 8.3 + - - +
159F LEU* 1.3 76.8 - - - +
161F ARG* 1.3 58.9 + - - +
163F ILE* 3.1 11.5 + - - +
164F ARG* 3.0 52.0 + - - +
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Residues in contact with ARG 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E GLN* 3.5 39.2 + - - +
26E ASN 5.3 0.2 + - - -
27E HIS* 4.1 16.3 + - - +
46F ILE* 3.8 16.8 - - + +
47F ASP* 2.9 42.6 + - - +
154F ASP* 4.2 2.0 + - - -
157F TYR* 3.0 28.2 + - - +
158F THR* 3.5 29.6 + - + +
160F VAL* 1.3 72.7 - - - +
162F GLU* 1.3 65.3 + - + +
164F ARG* 3.4 13.7 + - - +
165F LYS* 3.1 35.4 + - + +
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Residues in contact with GLU 162 (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* 4.1 15.8 - - + +
111F MET 4.1 12.5 + - - +
112F VAL* 4.2 3.4 - - + -
138F GLY 4.8 6.1 - - - +
139F ILE* 5.1 1.4 - - - +
140F PRO* 3.5 39.0 - - + +
158F THR* 2.9 19.6 + - - +
159F LEU* 3.3 10.1 - - - +
161F ARG* 1.3 79.4 - - - +
163F ILE* 1.3 60.0 + - - +
165F LYS* 3.0 46.3 + - - +
166F HIS* 3.5 14.4 + - - +
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Residues in contact with ILE 163 (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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4F TYR* 3.8 27.4 - - + -
6F LEU* 3.4 32.5 - - + -
76F GLU* 3.9 21.3 - - + +
77F GLY* 3.8 15.9 - - - +
110F PRO* 3.7 24.9 - - + -
159F LEU* 2.9 18.1 + - + +
160F VAL* 3.1 9.8 + - - +
162F GLU* 1.3 75.0 - - - +
164F ARG* 1.3 64.0 + - - +
166F HIS* 3.3 5.4 + - + +
167F LYS* 3.3 33.3 + - + +
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Residues in contact with ARG 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F TYR* 3.1 27.6 + - + +
46F ILE* 3.0 38.1 + - - +
47F ASP* 3.6 14.6 + - - +
49F GLU* 3.1 50.0 + - - +
51F CYS* 3.5 18.6 - - - -
160F VAL* 3.0 25.0 + - - +
161F ARG* 3.7 13.8 - - - +
162F GLU 3.3 0.4 - - - -
163F ILE* 1.3 72.8 - - - +
165F LYS* 1.3 63.9 + - + +
166F HIS 3.0 5.5 + - - -
167F LYS* 3.3 25.7 + - - +
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Residues in contact with LYS 165 (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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161F ARG* 3.1 19.6 + - - +
162F GLU* 3.0 41.8 + - - +
164F ARG* 1.3 80.4 - - + +
166F HIS* 1.3 59.4 + - - +
167F LYS 4.4 2.8 - - - +
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Residues in contact with HIS 166 (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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106F SER* 5.2 1.1 - - - -
108F ASP* 2.9 52.0 + - + +
110F PRO* 3.9 23.0 - - + +
162F GLU 3.7 9.9 - - - +
163F ILE* 3.6 10.1 - - + +
164F ARG 3.0 0.4 - - - -
165F LYS* 1.3 82.1 - - - +
167F LYS* 1.3 67.3 + - + +
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Residues in contact with LYS 167 (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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2F THR* 4.1 14.6 - - - +
3F GLU 4.3 2.6 + - - -
4F TYR* 3.7 37.7 - - - -
76F GLU* 4.2 17.6 + - - +
163F ILE* 3.3 21.5 + - + +
164F ARG* 3.3 15.9 + - - +
165F LYS 4.4 2.6 - - - +
166F HIS* 1.3 88.8 - - + +
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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