Contacts of the helix formed by residues 70 - 84 (chain F) in PDB entry 3V5I
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 SER 70 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36F ILE* 2.9 14.0 + - - +
37F ASP* 4.5 5.4 - - - -
38F ASP* 4.4 4.4 + - - -
69F GLY* 1.3 70.7 - - - -
71F VAL* 1.3 59.0 + - - +
72F THR* 3.4 10.2 + - - -
73F ALA* 3.0 29.9 + - - +
74F GLY* 2.8 26.7 + - - -
99F MET* 4.1 3.2 - - - +
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Residues in contact with VAL 71 (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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69F GLY 3.4 5.7 + - - +
70F SER* 1.3 71.6 + - - +
72F THR* 1.3 62.4 + - + +
74F GLY* 3.3 1.7 + - - -
75F PHE* 2.9 53.2 + - + -
99F MET* 3.7 28.2 - - + +
125F PRO* 4.4 15.9 - - + -
126F LEU 6.0 1.6 - - - +
146F THR* 3.7 22.9 - - + -
150F LEU* 4.3 10.1 - - + -
119G GLU* 6.0 0.7 - - - +
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Residues in contact with THR 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F ASP* 4.7 4.9 + - - -
70F SER* 3.4 8.0 + - - -
71F VAL* 1.3 83.0 - - + +
73F ALA* 1.3 64.6 + - - +
75F PHE* 3.0 16.6 + - + +
76F ALA 3.0 10.0 + - - -
142F HIS* 6.0 1.6 - - + -
65G ASN* 5.0 1.7 + - - -
94G GLY* 3.5 18.8 - - - +
95G MET* 4.0 34.6 - - + +
119G GLU* 3.8 25.1 - - - +
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Residues in contact with ALA 73 (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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36F ILE* 3.8 8.7 - - + -
37F ASP 3.7 20.0 - - - -
38F ASP* 3.6 18.8 + - - +
41F ALA* 3.3 24.8 - - + +
70F SER* 3.0 27.0 + - - +
72F THR* 1.3 77.9 + - - +
74F GLY* 1.3 62.8 + - - +
76F ALA* 3.2 11.2 + - - -
77F ILE* 3.4 6.1 + - - +
65G ASN* 4.7 2.2 - - - +
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Residues in contact with GLY 74 (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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36F ILE* 3.8 8.9 - - - +
70F SER 2.8 14.9 + - - -
71F VAL 3.7 3.6 - - - -
72F THR 3.2 0.2 - - - -
73F ALA* 1.3 77.9 - - - +
75F PHE* 1.3 57.8 + - - +
77F ILE* 3.1 7.7 + - - +
78F TYR* 2.8 27.6 + - - +
99F MET* 3.8 21.5 - - - -
103F LEU* 3.6 11.1 - - - +
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Residues in contact with PHE 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71F VAL* 2.9 43.3 + - + -
72F THR* 3.0 10.9 + - + +
74F GLY* 1.3 73.8 - - - +
76F ALA* 1.3 60.6 + - - +
78F TYR* 3.7 14.1 - + + +
79F ASP* 2.8 34.7 + - - +
99F MET* 5.2 0.9 - - - -
102F PHE* 3.7 23.3 - + - -
146F THR* 5.2 0.7 - - + -
149F LYS* 3.5 37.5 - - + -
150F LEU* 3.6 26.5 - - + -
153F ILE* 3.8 16.2 - - + -
94G GLY* 4.8 5.8 + - - +
117G ASN* 3.6 32.3 - - + +
119G GLU* 5.9 0.7 - - - -
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Residues in contact with ALA 76 (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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41F ALA* 4.5 3.1 - - + -
45F VAL* 4.0 10.8 - - + -
72F THR 3.0 6.9 + - - +
73F ALA 3.6 9.2 - - - +
74F GLY 3.2 0.2 - - - -
75F PHE* 1.3 76.6 - - - +
77F ILE* 1.3 57.8 + - - +
79F ASP* 4.2 1.9 - - - +
80F THR* 2.8 34.7 + - - -
65G ASN* 4.1 13.9 - - - +
93G ILE* 4.1 16.7 - - + +
94G GLY* 3.8 28.0 - - - +
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Residues in contact with ILE 77 (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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32F LEU* 5.1 4.0 - - + -
36F ILE* 4.5 13.7 - - + -
40F VAL* 5.1 0.9 - - + -
41F ALA* 3.9 30.1 - - + +
44F ILE* 3.9 38.1 - - + -
45F VAL* 4.2 5.6 - - + -
48F LEU* 4.5 1.5 - - + +
62F LEU* 5.0 3.1 - - + -
73F ALA 3.4 11.6 + - - +
74F GLY 3.1 6.6 + - - +
76F ALA* 1.3 76.2 - - - +
78F TYR* 1.3 66.8 + - - +
80F THR* 3.1 3.6 + - - -
81F ILE* 2.9 42.0 + - + +
103F LEU* 4.0 26.0 - - + -
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Residues in contact with TYR 78 (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 GLY 2.8 19.2 + - - +
75F PHE* 3.7 15.5 - + + +
77F ILE* 1.3 75.2 - - - +
79F ASP* 1.3 77.2 + - - +
81F ILE* 3.1 8.3 + - - +
82F GLN* 3.1 41.3 + - + +
102F PHE* 3.6 17.9 - + + -
103F LEU* 3.8 10.2 - - + +
106F ALA* 3.3 33.9 - - + -
153F ILE* 3.3 27.4 - - + +
156F GLU* 5.3 2.1 + - - -
157F ARG* 3.2 27.0 + - - -
117G ASN* 3.6 19.1 - - - -
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Residues in contact with ASP 79 (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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75F PHE 2.8 20.3 + - - +
76F ALA* 4.3 2.0 - - - +
78F TYR* 1.3 85.6 - - - +
80F THR* 1.3 56.6 + - - +
82F GLN* 3.3 5.4 + - - +
83F HIS* 2.9 30.7 + - - +
93G ILE* 5.9 0.4 - - + -
94G GLY 5.8 1.4 + - - +
115G LEU* 3.3 34.4 - - + +
116G PRO* 3.8 10.3 - - + +
117G ASN* 2.6 57.7 + - - +
118G ALA* 3.4 3.8 + - - +
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Residues in contact with THR 80 (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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45F VAL* 3.6 29.4 - - + +
48F LEU* 3.9 29.4 - - + -
49F LEU* 4.4 9.0 - - + -
76F ALA 2.8 22.2 + - - -
77F ILE 3.1 5.2 + - - -
79F ASP* 1.3 74.5 - - - +
81F ILE* 1.3 66.0 + - - +
83F HIS* 3.1 15.6 + - + +
84F ILE* 3.1 25.2 + - + +
93G ILE* 4.6 4.2 - - - +
115G LEU* 4.3 10.1 - - + +
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Residues in contact with ILE 81 (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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48F LEU* 3.9 15.9 - - + -
62F LEU* 4.1 20.6 - - + -
77F ILE* 2.9 35.1 + - + +
78F TYR* 3.5 10.5 - - - +
80F THR* 1.3 78.4 - - - +
82F GLN* 1.3 77.8 + - - +
83F HIS 3.3 0.3 + - - -
84F ILE* 3.5 21.4 + - - +
86F PRO 4.8 1.9 - - - +
88F VAL* 4.0 31.3 - - + +
90F THR* 5.3 2.0 - - + -
103F LEU* 4.8 9.6 - - + +
106F ALA* 3.8 20.0 - - + +
107F GLY* 5.1 0.7 - - - -
108F ALA 5.6 1.3 - - - +
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Residues in contact with GLN 82 (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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78F TYR* 3.1 49.1 + - + +
79F ASP* 3.9 6.7 - - - +
81F ILE* 1.3 84.6 + - - +
83F HIS* 1.3 60.9 + - - +
84F ILE 4.0 4.5 - - - +
106F ALA* 3.1 24.8 + - - +
107F GLY 6.0 0.4 - - - -
108F ALA* 6.3 0.6 - - - +
157F ARG* 3.6 23.4 + - - +
192G PRO* 3.8 32.5 - - + +
193G GLU 4.2 5.4 + - - -
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Residues in contact with HIS 83 (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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49F LEU* 5.3 6.4 - - + +
52F GLN* 4.7 3.5 + - - -
79F ASP 2.9 17.7 + - - +
80F THR* 3.1 7.9 + - - +
82F GLN* 1.3 78.9 - - - +
84F ILE* 1.3 70.5 + - + +
63G TYR* 5.4 6.5 - + - -
115G LEU* 4.5 10.4 - - + +
116G PRO* 6.4 1.1 - - + -
190G MET* 3.3 49.4 - - + +
191G VAL 4.6 11.0 - - - -
192G PRO* 4.7 3.4 - - + -
193G GLU* 3.9 32.8 + - + +
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Residues in contact with ILE 84 (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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48F LEU* 4.1 22.4 - - + +
49F LEU* 4.2 19.3 - - + -
52F GLN* 3.5 29.2 - - + +
60F ILE* 3.8 29.4 - - + -
80F THR* 3.1 21.1 + - + +
81F ILE 3.5 14.6 - - - +
82F GLN 4.0 4.5 - - - +
83F HIS* 1.3 87.0 - - - +
85F LYS* 1.3 62.7 + - - +
86F PRO* 3.9 13.7 - - + +
88F VAL* 4.0 13.9 - - + -
193G GLU* 5.3 3.5 - - - -
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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
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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