Contacts of the helix formed by residues 102 - 116 (chain C) in PDB entry 1VLA
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 102 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63C VAL* 3.9 33.9 - - + -
66C GLN* 4.3 8.1 - - - +
97C PHE* 3.4 37.7 - - + -
100C GLU 3.4 3.6 - - - +
101C PRO* 1.3 80.8 - - + +
103C LYS* 1.3 61.9 + - - +
104C ASP* 3.4 2.5 - - - -
105C LYS* 3.1 14.6 + - + -
106C VAL* 3.0 23.4 + - + +
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Residues in contact with LYS 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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101C PRO* 2.9 39.0 + - + +
102C PRO* 1.3 67.7 - - - +
104C ASP* 1.3 62.2 + - - +
106C VAL* 3.3 1.5 + - - +
107C GLU* 2.8 47.2 + - - +
136C TYR* 3.5 47.3 + - + +
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Residues in contact with ASP 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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102C PRO 3.4 0.4 - - - -
103C LYS* 1.3 78.0 - - - +
105C LYS* 1.3 60.2 + - + +
107C GLU* 3.3 16.8 + - - +
108C LYS* 3.0 28.8 + - - +
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Residues in contact with LYS 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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58C LEU* 4.1 7.0 - - + -
61C MSE 3.0 56.0 + - + +
62C LYS* 5.2 0.4 + - - +
63C VAL* 3.9 24.0 - - + +
102C PRO* 3.1 16.6 + - + +
104C ASP* 1.3 77.4 - - + +
106C VAL* 1.3 57.8 + - - +
108C LYS* 3.3 6.2 + - - +
109C ALA* 2.9 30.0 + - - +
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Residues in contact with VAL 106 (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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58C LEU* 4.0 15.9 - - + -
95C PHE* 3.3 41.5 - - + -
97C PHE* 3.6 33.2 - - + -
102C PRO* 3.0 18.7 + - + +
103C LYS 3.7 1.3 - - - +
105C LYS* 1.3 75.0 - - - +
107C GLU* 1.3 64.3 + - - +
109C ALA* 3.4 1.8 + - - +
110C VAL* 3.0 24.8 + - + +
134C ILE* 4.3 4.5 - - + -
136C TYR* 3.6 22.9 - - + +
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Residues in contact with GLU 107 (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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103C LYS* 2.8 35.7 + - - +
104C ASP* 3.7 16.8 - - - +
106C VAL* 1.3 75.8 - - - +
108C LYS* 1.3 58.1 + - - +
110C VAL* 3.5 1.7 + - - +
111C GLN* 2.8 38.4 + - + +
134C ILE* 3.8 23.3 - - + -
136C TYR* 4.6 4.7 + - - +
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Residues in contact with LYS 108 (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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61C MSE 3.8 18.8 - - + -
104C ASP 3.0 17.1 + - - +
105C LYS* 3.5 7.0 - - - +
106C VAL 3.2 0.2 - - - -
107C GLU* 1.3 74.5 - - - +
109C ALA* 1.3 55.0 + - - +
111C GLN* 3.2 7.6 + - + +
112C LEU* 2.8 48.5 + - + +
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Residues in contact with ALA 109 (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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54C VAL* 4.3 11.2 - - + +
57C ILE* 3.5 42.5 - - + +
58C LEU* 4.1 18.8 - - + -
61C MSE 4.2 0.4 - - - +
105C LYS 2.9 16.1 + - - +
106C VAL 3.8 3.4 - - - +
108C LYS* 1.3 74.7 - - - +
110C VAL* 1.3 57.9 + - - +
112C LEU* 3.2 4.2 + - - +
113C SER* 3.0 26.7 + - - -
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Residues in contact with VAL 110 (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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54C VAL* 4.1 11.7 - - + -
93C TYR* 3.9 30.7 - - + -
95C PHE* 3.9 26.0 - - + -
106C VAL 3.0 20.0 + - - +
107C GLU 3.9 2.9 - - - +
109C ALA* 1.3 75.3 - - - +
111C GLN* 1.3 56.8 + - - +
113C SER* 3.4 1.7 + - - -
114C GLN* 2.9 29.2 + - - +
132C TYR* 3.7 30.7 - - + -
134C ILE* 4.0 20.6 - - + -
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Residues in contact with GLN 111 (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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107C GLU* 2.8 27.1 + - + +
108C LYS* 3.4 8.7 - - + +
110C VAL* 1.3 74.5 - - - +
112C LEU* 1.3 58.6 + - + +
115C GLU* 2.7 60.4 + - + +
132C TYR* 2.4 41.0 + - - -
134C ILE* 6.2 1.2 - - - +
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Residues in contact with LEU 112 (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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57C ILE* 3.8 35.4 - - + -
61C MSE 4.4 7.6 - - + -
108C LYS* 2.8 33.3 + - + +
109C ALA 3.5 4.0 - - - +
111C GLN* 1.3 74.0 - - + +
113C SER* 1.3 59.5 + - - +
116C LYS* 3.0 28.0 + - + +
117C TYR* 2.8 44.8 + - + +
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Residues in contact with SER 113 (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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50C THR* 2.7 31.1 + - - -
53C ASP* 2.7 39.5 + - - +
54C VAL* 4.2 6.5 - - - -
57C ILE* 4.5 0.2 - - - +
109C ALA 3.0 15.3 + - - -
110C VAL* 3.8 4.3 - - - -
112C LEU* 1.3 74.6 - - - +
114C GLN* 1.3 59.2 + - - +
117C TYR* 3.7 5.0 - - - +
118C CYS 2.9 23.4 + - - -
119C SER* 3.0 13.5 + - - -
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Residues in contact with GLN 114 (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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50C THR* 4.4 1.6 + - - -
91C LEU* 3.3 24.4 - - - +
93C TYR* 2.6 32.3 + - + +
110C VAL 2.9 19.5 + - - +
111C GLN 4.1 0.2 - - - +
113C SER* 1.3 77.9 - - - +
115C GLU* 1.3 61.2 + - - +
118C CYS* 3.3 20.4 - - - +
120C VAL* 4.5 13.7 + - - +
121C SER* 3.9 10.2 + - - -
130C VAL* 4.5 12.8 - - - +
132C TYR* 3.5 52.4 - - + +
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Residues in contact with GLU 115 (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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111C GLN* 2.7 42.8 + - + +
114C GLN* 1.3 76.7 - - - +
116C LYS* 1.3 59.6 + - + +
117C TYR 3.8 0.2 - - - -
118C CYS* 3.4 16.3 - - - -
129C LYS* 6.1 1.0 - - - +
132C TYR* 2.7 30.2 + - - +
83D PRO* 5.3 0.7 - - - +
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Residues in contact with LYS 116 (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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111C GLN 3.6 0.4 + - - +
112C LEU* 3.0 32.9 + - + +
115C GLU* 1.3 78.0 - - + +
117C TYR* 1.3 79.5 + - + +
118C CYS* 4.3 0.2 - - - -
82D HIS* 3.7 16.7 - - + +
83D PRO* 3.7 15.1 - - - +
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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