Contacts of the helix formed by residues 98 - 105 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67E PRO 4.0 10.8 - - - +
68E GLY* 4.3 3.1 - - - -
69E GLY 5.2 2.0 - - - +
97E ALA* 1.3 72.7 - - + +
99E MET* 1.3 61.9 + - - +
101E SER* 2.8 29.9 + - - -
102E PHE* 3.0 5.7 + - - +
121E MET* 2.9 16.8 + - + -
123E HIS* 3.3 40.2 - - + +
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Residues in contact with MET 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E ILE* 4.1 13.9 - - + -
68E GLY* 4.1 0.6 - - - -
69E GLY 4.2 17.3 - - - +
70E SER 3.9 6.1 - - - +
71E VAL* 3.6 41.5 - - + +
74E GLY* 3.7 26.9 - - - -
75E PHE* 5.2 0.9 - - - -
98E ALA* 1.3 81.3 - - + +
100E GLY* 1.3 55.1 + - - +
102E PHE* 3.3 30.2 + - + +
103E LEU* 2.9 30.4 + - + +
150E LEU* 3.7 25.4 - - + -
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Residues in contact with GLY 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E ILE* 4.0 12.7 - - - +
64E ILE* 4.0 9.7 - - - +
66E SER* 4.3 13.9 - - - -
68E GLY* 3.8 4.8 - - - -
96E ALA* 4.0 6.7 - - - -
97E ALA 2.7 16.3 + - - -
99E MET* 1.3 77.4 - - - +
101E SER* 1.3 55.2 + - - -
103E LEU* 3.3 6.6 + - - +
104E LEU* 3.0 24.9 + - - +
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Residues in contact with SER 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E ALA* 3.2 22.9 - - - -
97E ALA 3.4 3.8 + - - -
98E ALA* 2.8 18.7 + - - -
100E GLY* 1.3 69.2 - - - -
102E PHE* 1.3 65.1 + - - +
104E LEU* 3.3 9.9 + - - +
105E ALA* 3.0 24.6 + - - +
120E VAL* 3.6 21.1 - - - -
121E MET 3.3 12.5 + - - -
122E ILE* 3.4 15.4 - - - +
154E LEU* 5.7 0.4 - - - +
185E LEU* 4.6 7.0 - - - +
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Residues in contact with PHE 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74E GLY 5.6 0.2 - - - -
75E PHE* 3.8 28.7 - + - -
78E TYR* 3.5 27.1 - + + -
98E ALA 3.0 7.3 + - - +
99E MET* 3.3 37.0 - - + +
101E SER* 1.3 79.0 + - - +
103E LEU* 1.3 67.9 + - + +
105E ALA* 3.3 4.7 + - - +
106E ALA* 3.2 17.0 + - - +
150E LEU* 3.7 38.1 - - + -
153E ILE* 3.7 27.1 - - + -
154E LEU* 4.0 26.7 - - + -
157E ARG* 5.8 0.7 - - - -
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Residues in contact with LEU 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E LEU* 4.3 10.8 - - + -
36E ILE* 3.8 28.3 - - + -
62E LEU* 5.5 1.8 - - + -
64E ILE* 4.0 12.6 - - + -
74E GLY* 3.5 26.2 - - - +
77E ILE* 3.9 31.0 - - + -
78E TYR* 3.7 24.9 - - + +
81E ILE* 4.8 9.0 - - + +
90E THR* 3.8 7.1 - - - +
99E MET* 2.9 14.4 + - + +
100E GLY* 3.7 6.3 - - - +
101E SER 3.2 0.2 - - - -
102E PHE* 1.3 78.1 - - + +
104E LEU* 1.3 62.9 + - - +
106E ALA* 2.8 24.0 + - + +
107E GLY 3.6 3.5 + - - -
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Residues in contact with LEU 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64E ILE* 3.6 13.1 - - + +
90E THR* 2.7 36.9 + - - +
91E ILE 4.3 0.7 - - - -
92E CYS* 3.6 32.5 - - + +
96E ALA* 4.1 7.2 - - + -
100E GLY 3.0 13.8 + - - +
101E SER* 3.4 11.7 - - - +
103E LEU* 1.3 75.7 - - - +
105E ALA* 1.3 60.4 + - - +
106E ALA 3.3 1.2 + - - -
107E GLY 3.5 1.4 + - - -
112E ARG* 3.6 5.9 - - - +
113E PHE 3.5 22.2 - - - +
120E VAL* 3.9 23.8 - - + -
185E LEU* 4.5 4.9 - - + +
186E ILE* 3.7 23.3 - - + -
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Residues in contact with ALA 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E SER 3.0 13.1 + - - +
102E PHE 3.7 5.4 - - - +
103E LEU 3.1 0.4 - - - -
104E LEU* 1.3 77.4 - - - +
106E ALA* 1.3 58.2 + - - +
107E GLY 3.3 0.7 - - - -
112E ARG* 2.9 26.7 + - - +
154E LEU* 4.3 12.6 - - + -
157E ARG* 3.5 19.2 + - + -
158E THR* 5.0 1.3 - - + -
185E LEU* 3.4 40.6 - - + +
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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