Contacts of the helix formed by residues 144 - 156 (chain F) in PDB entry 4GOM
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 144 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7F PHE* 3.7 40.2 - - + +
81F PHE* 4.5 3.6 - - + -
112F LEU* 4.3 11.2 - - + -
116F ARG* 4.1 13.5 - - + +
142F TYR* 3.2 24.4 - - + +
143F PHE* 1.3 85.6 - - + +
145F GLU* 1.3 57.7 + - - +
146F ALA 3.5 1.8 - - - -
147F GLU* 3.3 15.8 + - + +
148F LEU* 2.9 37.6 + - + +
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Residues in contact with GLU 145 (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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74F VAL* 4.4 4.7 - - + -
78F ARG* 2.8 45.9 + - - -
142F TYR* 4.5 0.8 + - - -
143F PHE* 2.8 32.5 + - + +
144F PRO* 1.3 70.0 - - - +
146F ALA* 1.3 64.9 + - - +
147F GLU* 3.2 0.5 + - - -
148F LEU* 3.2 7.1 + - - +
149F TYR* 3.2 44.3 + - + -
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Residues in contact with ALA 146 (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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142F TYR* 4.6 4.6 + - - +
144F PRO 3.5 0.4 - - - -
145F GLU* 1.3 78.3 - - - +
147F GLU* 1.3 70.3 + - - +
149F TYR* 3.3 7.1 + - - +
150F HIS* 3.0 29.9 + - - +
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Residues in contact with GLU 147 (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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5F ARG* 3.3 49.1 - - + +
6F ALA 4.2 3.8 - - - +
7F PHE* 3.7 21.7 + - + +
43F LEU* 5.4 0.7 - - - +
142F TYR* 2.6 41.9 + - - -
144F PRO* 3.7 5.5 - - + +
145F GLU 3.2 0.4 - - - -
146F ALA* 1.3 83.9 + - - +
148F LEU* 1.3 67.3 + - - +
150F HIS* 3.9 5.7 + - - +
151F PHE* 3.0 26.0 + - - +
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Residues in contact with LEU 148 (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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7F PHE* 3.7 35.9 - - + -
66F VAL* 3.9 20.9 - - + +
70F THR* 5.6 0.7 - - - -
73F TYR* 3.7 27.8 - - + -
74F VAL* 4.4 19.7 - - + -
112F LEU* 4.1 14.6 - - + -
143F PHE* 4.0 27.4 - - + -
144F PRO* 2.9 22.2 + - + +
145F GLU* 3.2 5.4 + - - +
147F GLU* 1.3 77.7 - - - +
149F TYR* 1.4 57.8 + - - +
151F PHE* 3.7 4.0 - - - +
152F ALA* 3.1 27.9 + - - +
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Residues in contact with TYR 149 (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 THR* 3.7 27.4 - - + -
71F ASP* 2.9 26.8 + - - -
74F VAL* 3.9 26.7 - - + +
78F ARG* 4.9 3.3 + - - -
145F GLU* 3.2 48.7 + - + -
146F ALA* 3.9 8.5 - - - +
148F LEU* 1.4 73.3 - - - +
150F HIS* 1.3 67.4 + - - +
151F PHE 3.2 0.5 + - - -
152F ALA* 3.2 4.8 + - + +
153F GLU* 3.0 25.1 + - - +
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Residues in contact with HIS 150 (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 ASN* 3.5 42.0 + - - +
5F ARG 5.4 2.0 + - - -
43F LEU* 3.4 41.7 + - + +
146F ALA 3.0 17.2 + - - +
147F GLU* 4.1 5.5 + - - +
149F TYR* 1.3 77.5 - - - +
151F PHE* 1.3 60.8 + - - +
153F GLU* 3.8 15.9 - - + +
154F LYS* 3.1 44.0 + - + +
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Residues in contact with PHE 151 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7F PHE* 3.8 26.2 - + + -
36F VAL* 6.1 0.2 - - + -
38F ALA 4.1 12.6 - - - -
39F GLY* 4.9 0.9 - - - -
42F PHE* 3.9 23.7 - + - -
43F LEU* 3.9 29.8 - - + -
63F TYR* 3.5 54.5 - + + -
66F VAL* 4.1 10.8 - - + -
147F GLU 3.0 20.0 + - - +
148F LEU 3.7 3.8 - - - +
150F HIS* 1.3 76.9 + - - +
152F ALA* 1.3 54.5 + - - +
154F LYS* 3.4 2.8 + - - +
155F ALA* 2.7 39.6 + - + +
160F PHE* 3.8 22.2 - + - -
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Residues in contact with ALA 152 (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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66F VAL* 3.6 14.6 - - + +
70F THR* 3.5 37.0 - - + +
148F LEU 3.1 13.8 + - - +
149F TYR* 3.4 9.4 - - + +
151F PHE* 1.3 75.0 - - - +
153F GLU* 1.3 66.4 - - - +
155F ALA* 3.1 16.8 + - - +
156F GLN* 3.0 23.1 + - - +
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Residues in contact with GLU 153 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149F TYR 3.0 16.7 + - - +
150F HIS* 3.8 15.6 - - + +
152F ALA* 1.3 74.2 - - - +
154F LYS* 1.3 66.5 + - + +
156F GLN* 3.1 27.6 + - - +
157F ASN* 4.6 2.3 + - - +
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Residues in contact with LYS 154 (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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42F PHE* 3.4 37.6 + - + +
43F LEU* 3.8 14.4 - - + +
45F THR 2.8 28.4 + - - -
46F ASP* 4.6 2.8 - - - +
47F PHE 5.2 0.6 + - - -
50F TYR* 3.0 24.0 + - + -
150F HIS* 3.1 39.7 + - + +
151F PHE* 3.8 4.9 - - - +
153F GLU* 1.3 84.7 - - + +
155F ALA* 1.3 59.4 + - - +
156F GLN 3.1 1.3 + - - -
157F ASN* 3.5 16.0 + - - +
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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
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42F PHE* 3.8 9.0 - - - -
67F LYS* 3.4 34.8 - - + -
151F PHE* 2.7 26.3 + - + +
152F ALA* 3.1 13.4 + - - +
154F LYS* 1.3 68.3 - - - +
156F GLN* 1.3 62.6 + - - +
157F ASN 3.1 3.1 - - - -
158F ALA* 3.0 17.6 + - - +
160F PHE* 4.0 18.6 - - + -
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Residues in contact with GLN 156 (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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67F LYS* 3.1 46.9 + - - +
68F MET* 5.5 2.6 - - - +
70F THR* 4.7 3.2 + - - -
152F ALA* 3.0 20.7 + - - +
153F GLU* 3.1 21.0 + - - +
155F ALA* 1.3 77.7 - - - +
157F ASN* 1.3 68.5 + - - +
158F ALA 3.4 1.4 + - - -
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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
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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