Contacts of the helix formed by residues 98 - 105 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C PRO 4.0 11.0 - - - +
68C GLY* 4.3 3.1 - - - -
69C GLY 5.0 2.9 - - - +
97C ALA* 1.3 74.3 - - + +
99C MET* 1.3 63.2 + - - +
101C SER* 2.8 30.3 + - - -
102C PHE* 3.1 5.4 + - - +
121C MET* 3.0 14.9 + - + -
122C ILE* 5.1 2.2 - - - +
123C HIS* 3.3 39.0 + - + +
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Residues in contact with MET 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C ILE* 4.1 9.4 - - + -
68C GLY* 4.1 0.2 - - - -
69C GLY 4.1 21.8 - - - +
70C SER 4.0 6.7 - - - +
71C VAL* 3.6 43.1 - - + +
74C GLY* 3.7 25.8 - - - -
75C PHE* 4.8 1.1 - - - -
98C ALA* 1.3 79.6 - - - +
100C GLY* 1.3 62.1 + - - +
102C PHE* 3.3 30.6 - - + +
103C LEU* 3.0 24.8 + - + +
150C LEU* 3.7 25.8 - - + -
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Residues in contact with GLY 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C ILE* 4.2 12.3 - - - -
64C ILE* 4.1 10.7 - - - +
66C SER* 4.4 13.5 - - - -
68C GLY* 3.7 4.9 - - - -
96C ALA* 4.1 7.0 - - - -
97C ALA 2.8 16.9 + - - -
99C MET* 1.3 77.6 - - - +
101C SER* 1.3 55.5 + - - -
103C LEU* 3.2 6.2 + - - +
104C LEU* 3.0 24.4 + - - +
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Residues in contact with SER 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C ALA* 3.3 23.9 - - - -
97C ALA 3.5 4.2 + - - -
98C ALA 2.8 19.3 + - - -
100C GLY* 1.3 69.6 - - - -
102C PHE* 1.3 65.2 + - - +
104C LEU* 3.2 10.7 + - - +
105C ALA* 3.0 23.7 + - - +
120C VAL* 3.7 17.0 - - - -
121C MET 3.3 15.7 + - - -
122C ILE* 3.3 16.1 - - - +
154C LEU* 5.8 0.2 - - - -
185C LEU* 4.5 5.8 - - - +
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Residues in contact with PHE 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C PHE* 3.7 27.8 - + - -
78C TYR* 3.5 28.3 - + + -
98C ALA 3.1 2.6 + - - +
99C MET* 3.3 36.3 - - + +
101C SER* 1.3 82.5 + - - +
103C LEU* 1.3 66.9 + - + +
105C ALA* 3.3 5.9 + - - +
106C ALA* 3.2 19.4 + - - +
150C LEU* 3.7 37.2 - - + -
153C ILE* 3.7 27.6 - - + -
154C LEU* 4.0 27.5 - - + +
157C ARG* 5.8 1.2 - - - -
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Residues in contact with LEU 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C LEU* 4.1 13.0 - - + -
36C ILE* 3.9 26.2 - - + -
62C LEU* 5.5 2.2 - - + -
64C ILE* 4.0 11.2 - - + -
74C GLY* 3.6 24.5 - - - +
77C ILE* 4.0 31.0 - - + -
78C TYR* 3.8 24.9 - - + +
81C ILE* 4.8 8.5 - - + +
90C THR* 3.7 8.1 - - - +
99C MET* 3.0 15.2 + - + +
100C GLY 3.2 6.7 + - - +
102C PHE* 1.3 78.8 - - + +
104C LEU* 1.3 66.5 + - - +
106C ALA* 2.9 17.3 + - - +
107C GLY 3.6 3.6 + - - -
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Residues in contact with LEU 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C ILE* 3.7 12.9 - - + +
90C THR* 2.7 36.4 + - - +
91C ILE 4.4 0.7 - - - -
92C CYS* 3.6 32.5 - - + +
96C ALA* 4.0 7.9 - - + -
100C GLY 3.0 12.0 + - - +
101C SER* 3.2 11.4 + - - +
103C LEU* 1.3 76.0 - - - +
105C ALA* 1.3 57.5 + - - +
106C ALA 3.1 4.3 + - - -
107C GLY 3.4 1.9 + - - -
112C ARG* 3.6 6.1 - - - +
113C PHE 3.5 22.7 - - - +
120C VAL* 3.8 26.5 - - + -
185C LEU* 4.7 5.2 - - + +
186C ILE* 3.8 24.5 - - + -
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Residues in contact with ALA 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C SER 3.0 15.5 + - - +
102C PHE 3.7 6.1 - - - +
103C LEU 3.2 0.2 - - - -
104C LEU* 1.3 76.2 - - - +
106C ALA* 1.3 56.8 + - - +
107C GLY 3.4 0.7 - - - -
112C ARG* 2.9 26.9 + - - +
154C LEU* 4.3 12.6 - - + -
157C ARG* 3.5 18.8 + - + -
158C THR* 5.0 1.1 - - + -
185C LEU* 3.3 41.3 - - + +
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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