Contacts of the helix formed by residues 109 - 118 (chain C) in PDB entry 3VTW
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 109 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71C ASP 3.7 14.4 - - - +
72C HIS* 4.4 11.7 - - - +
73C VAL 3.6 7.0 - - - +
74C ASN* 4.0 4.9 - - + -
107C SER 4.1 4.0 - - - +
108C THR* 1.3 87.1 - - - +
110C ILE* 1.3 64.2 + - - +
111C SER* 2.9 10.8 + - - +
112C GLU* 2.8 42.1 + - - +
113C VAL* 3.3 8.9 + - - +
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Residues in contact with ILE 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ILE* 3.8 14.8 - - + -
48C VAL* 3.7 26.5 - - + -
69C VAL* 3.7 13.7 - - + -
70C PRO 3.5 22.2 - - - +
71C ASP 3.7 2.5 - - - +
73C VAL 2.8 21.9 + - - +
75C MET* 3.5 23.1 - - + +
78C LEU* 3.5 30.7 - - + -
108C THR 3.7 1.6 + - - -
109C PRO* 1.3 70.3 - - - +
111C SER* 1.3 59.4 + - - +
113C VAL* 3.6 2.4 - - - +
114C TYR* 2.8 28.2 + - - +
124C LEU* 3.8 18.4 - - + -
126C MET* 3.9 0.4 - - + -
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Residues in contact with SER 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ILE* 3.8 14.1 - - - +
71C ASP* 3.3 36.9 + - - -
109C PRO* 2.9 5.4 + - - +
110C ILE* 1.3 78.8 - - - +
112C GLU* 1.3 71.7 + - - +
114C TYR* 3.4 5.4 + - - +
115C GLU* 3.2 24.7 + - - +
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Residues in contact with GLU 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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108C THR* 4.5 9.8 - - - +
109C PRO* 2.8 41.9 + - + +
111C SER* 1.3 85.4 + - - +
113C VAL* 1.3 60.5 + - - +
115C GLU* 2.8 25.9 + - - +
116C SER* 3.2 14.6 + - - -
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Residues in contact with VAL 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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75C MET* 4.1 26.2 - - + -
98C VAL* 4.3 17.3 - - + -
103C MET* 5.5 6.5 - - + -
106C VAL* 5.2 2.9 - - + -
108C THR* 3.4 23.6 - - - +
109C PRO 3.3 6.7 + - - +
110C ILE* 3.6 10.1 - - - +
112C GLU* 1.3 75.9 - - - +
114C TYR* 1.3 57.1 + - - +
116C SER* 3.5 5.3 + - - +
117C GLU* 2.9 34.8 + - + +
124C LEU* 3.9 21.9 - - + +
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Residues in contact with TYR 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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35C VAL* 4.1 8.5 - - - +
39C ARG* 4.2 28.2 + - - +
46C ILE* 3.4 37.0 - - + -
47C PRO* 4.2 10.4 - - + +
110C ILE 2.8 17.7 + - - +
111C SER 3.4 6.5 - - - +
112C GLU 3.1 0.4 - - - -
113C VAL* 1.3 73.5 - - - +
115C GLU* 1.3 79.3 + - - +
118C LYS* 3.1 65.0 + - + +
122C GLY* 2.6 36.2 + - - -
124C LEU* 4.0 21.3 - - + -
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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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39C ARG* 5.3 3.3 + - - -
111C SER 3.2 10.9 + - - +
112C GLU* 2.8 13.8 + - - +
114C TYR* 1.3 92.3 - - - +
116C SER* 1.3 61.6 + - - +
118C LYS* 3.2 34.9 + - - +
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Residues in contact with SER 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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112C GLU 3.2 11.1 + - - -
113C VAL* 4.0 5.0 - - - -
115C GLU* 1.3 75.9 - - - +
117C GLU* 1.3 83.6 + - - +
118C LYS 3.8 2.2 + - - +
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Residues in contact with GLU 117 (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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98C VAL* 3.9 19.5 - - + +
99C ASN* 3.0 44.0 + - - +
101C HIS* 3.4 23.6 + - + -
103C MET* 6.4 1.1 - - + -
113C VAL* 2.9 21.5 + - + +
116C SER* 1.3 98.3 - - - +
118C LYS* 1.3 70.8 + - - +
119C ASP* 3.4 1.2 + - - +
124C LEU* 3.7 16.8 - - + +
125C TYR 5.5 0.9 + - - -
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Residues in contact with LYS 118 (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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39C ARG* 6.1 0.2 - - - +
99C ASN* 4.7 1.2 - - - +
114C TYR* 3.1 59.9 + - + +
115C GLU* 3.2 37.4 + - - +
116C SER 3.8 2.3 - - - +
117C GLU* 1.3 81.0 - - - +
119C ASP* 1.3 68.9 + - - +
122C GLY* 4.6 6.1 - - - -
123C PHE 3.7 8.1 - - - +
124C LEU* 3.9 6.7 - - - +
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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