Contacts of the helix formed by residues 98 - 105 (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 ALA 98 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67F PRO 4.0 11.2 - - - +
68F GLY* 4.3 2.5 - - - -
69F GLY 5.1 2.0 - - - +
97F ALA* 1.3 72.5 - - + +
99F MET* 1.3 69.1 + - - +
101F SER* 2.8 23.4 + - - -
102F PHE* 3.1 5.4 + - - +
121F MET* 2.9 16.7 + - + -
122F ILE* 5.1 2.2 - - - +
123F HIS* 3.3 39.3 + - + +
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Residues in contact with MET 99 (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* 4.2 9.0 - - + -
68F GLY* 4.0 0.4 - - - -
69F GLY 4.2 22.0 - - - +
70F SER 4.1 7.2 - - - +
71F VAL* 3.7 37.0 - - + +
74F GLY* 3.8 26.2 - - - -
75F PHE* 4.8 1.3 - - - -
98F ALA* 1.3 80.0 - - - +
100F GLY* 1.3 60.1 + - - +
102F PHE* 3.3 31.0 + - + +
103F LEU* 3.1 23.9 + - + +
150F LEU* 3.6 30.5 - - + -
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Residues in contact with GLY 100 (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* 4.1 11.9 - - - +
64F ILE* 4.0 8.6 - - - +
66F SER* 4.3 14.1 - - - -
68F GLY* 3.7 5.1 - - - -
96F ALA* 3.9 9.0 - - - +
97F ALA 2.8 22.1 + - - -
99F MET* 1.3 72.6 - - - +
101F SER* 1.3 56.2 + - - -
103F LEU* 3.4 4.7 + - - +
104F LEU* 3.1 24.3 + - - +
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Residues in contact with SER 101 (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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96F ALA* 3.3 21.9 - - - -
97F ALA 3.5 3.0 + - - -
98F ALA* 2.8 19.5 + - - -
100F GLY* 1.3 70.6 - - - -
102F PHE* 1.3 66.1 + - - +
104F LEU* 3.3 10.2 + - - +
105F ALA* 3.1 22.5 + - - +
120F VAL* 3.6 21.5 - - - -
121F MET 3.3 13.2 + - - -
122F ILE* 3.4 15.6 - - - +
154F LEU* 6.1 0.3 - - - +
185F LEU* 4.4 7.5 - - - +
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Residues in contact with PHE 102 (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* 3.7 35.2 - + - -
78F TYR* 3.6 26.9 - + + -
98F ALA 3.1 2.6 + - - +
99F MET* 3.3 36.8 - - + +
101F SER* 1.3 83.4 + - - +
103F LEU* 1.3 67.3 + - + +
105F ALA* 3.2 13.7 + - - +
106F ALA* 3.3 12.0 + - - +
150F LEU* 3.7 35.0 - - + -
153F ILE* 3.7 24.5 - - + -
154F LEU* 3.9 28.0 - - + -
157F ARG* 5.7 0.7 - - - -
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Residues in contact with LEU 103 (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* 4.2 11.7 - - + -
36F ILE* 3.7 28.0 - - + -
62F LEU* 5.4 2.7 - - + -
64F ILE* 4.0 10.8 - - + -
74F GLY* 3.6 25.6 - - - +
77F ILE* 4.0 30.1 - - + -
78F TYR* 3.8 24.7 - - + +
81F ILE* 4.8 7.8 - - + +
90F THR* 3.7 7.8 - - - +
99F MET* 3.1 11.7 + - + +
100F GLY* 3.8 6.3 - - - +
101F SER 3.3 0.2 - - - -
102F PHE* 1.3 80.0 - - + +
104F LEU* 1.3 67.6 + - - +
106F ALA* 2.9 18.2 + - + +
107F GLY 3.6 3.8 + - - -
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Residues in contact with LEU 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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64F ILE* 3.7 12.4 - - + +
90F THR* 2.8 36.3 + - - +
91F ILE 4.3 0.7 - - - -
92F CYS* 3.7 31.2 - - + +
96F ALA* 4.2 6.7 - - + -
100F GLY 3.1 15.0 + - - +
101F SER* 3.4 11.4 - - - +
103F LEU* 1.3 76.0 - - - +
105F ALA* 1.3 61.2 + - - +
106F ALA 3.1 1.2 + - - -
107F GLY 3.5 1.4 + - - -
112F ARG* 3.6 6.8 - - - +
113F PHE 3.6 21.3 - - - +
120F VAL* 3.9 24.2 - - + -
185F LEU* 4.4 4.3 - - + +
186F ILE* 3.6 26.0 - - + -
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Residues in contact with ALA 105 (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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101F SER 3.1 13.0 + - - +
102F PHE 3.6 9.2 - - - +
103F LEU 3.1 0.6 - - - -
104F LEU* 1.3 75.6 - - - +
106F ALA* 1.3 58.0 + - - +
107F GLY 3.4 0.2 - - - -
112F ARG* 3.0 27.3 + - - +
154F LEU* 4.2 13.0 - - + -
157F ARG* 3.5 18.4 + - + -
158F THR* 5.1 1.1 - - + -
185F LEU* 3.4 38.4 - - + +
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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