Contacts of the helix formed by residues 104 - 111 (chain C) in PDB entry 3DVA
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 ASP 104 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C GLN* 3.3 6.8 + - - -
100C PRO* 3.5 30.2 - - + +
101C GLY* 3.2 22.4 + - - +
103C ARG* 1.3 80.3 + - - +
105C VAL* 1.3 63.1 + - - +
107C GLN* 2.8 37.8 + - - +
108C ILE* 3.8 7.4 + - - +
170C TYR* 3.1 23.6 - - + +
171C THR* 5.3 0.7 - - - -
200C GLN* 2.6 27.8 + - - -
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Residues in contact with VAL 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C LEU* 5.8 4.3 - - + -
75C TYR* 6.1 6.7 - - + -
102C TYR 4.0 14.4 - - - +
103C ARG 3.2 1.5 + - - +
104C ASP* 1.3 74.4 - - - +
106C PRO* 1.3 75.1 - - + +
108C ILE* 3.1 15.9 - - + +
109C ILE* 3.1 29.8 + - + +
113C LEU* 5.4 0.2 - - + -
118C ALA* 3.8 31.2 - - + +
121C PHE* 4.4 13.5 - - + -
140C PRO* 3.8 24.2 - - + -
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Residues in contact with PRO 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C THR* 3.8 28.7 - - + +
59C LEU* 5.0 11.9 - - + -
78C THR* 3.9 13.5 - - + +
85C GLN* 3.4 19.5 - - - +
86C ILE* 4.0 10.1 - - + -
103C ARG 3.6 11.0 - - - +
104C ASP 3.5 3.6 - - - -
105C VAL* 1.3 92.8 - - + +
107C GLN* 1.3 65.5 + - - +
109C ILE* 3.1 18.4 + - + +
110C TRP* 3.0 23.3 + - + +
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Residues in contact with GLN 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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85C GLN* 3.3 49.5 - - - +
86C ILE* 5.0 0.9 - - - +
89C HIS* 3.6 18.4 - - + -
98C ILE* 4.4 14.8 - - + -
104C ASP* 2.8 52.1 + - + +
105C VAL 3.3 0.4 - - - -
106C PRO* 1.3 73.8 - - - +
108C ILE* 1.3 61.3 + - - +
110C TRP* 3.6 2.2 + - - +
111C HIS* 3.2 22.5 + - - +
170C TYR* 3.5 39.2 - - + +
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Residues in contact with ILE 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C ILE* 4.1 6.3 - - + -
100C PRO* 3.5 31.2 - - + -
104C ASP 3.8 0.2 + - - -
105C VAL* 3.1 25.1 - - + +
107C GLN* 1.3 74.4 - - - +
109C ILE* 1.3 62.4 + - - +
111C HIS* 3.4 8.1 + - - +
112C GLY 3.4 5.5 + - - -
113C LEU* 2.9 49.9 + - + +
131C ILE* 6.4 0.2 - - + -
137C VAL* 3.7 32.3 - - + +
138C LEU 4.2 6.1 - - - +
139C PRO* 4.8 1.3 - - + -
140C PRO* 3.8 33.2 - - + -
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Residues in contact with ILE 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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55C TYR* 6.0 5.4 - - + -
59C LEU* 5.0 8.5 - - + -
105C VAL* 3.1 25.4 + - + +
106C PRO* 3.1 10.5 + - + +
108C ILE* 1.3 76.9 - - - +
110C TRP* 1.3 73.2 + - + +
111C HIS 3.0 0.2 - - - -
112C GLY* 3.0 18.7 + - - -
113C LEU* 3.4 31.7 + - + +
114C PRO 4.3 2.2 - - - +
115C LEU* 4.3 23.3 - - + +
118C ALA* 3.2 33.9 - - + -
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Residues in contact with TRP 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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48C GLU* 5.0 2.5 - - - -
52C ARG* 3.7 65.1 + - + +
55C TYR* 3.7 46.2 - + + -
56C THR* 3.3 18.1 + - - -
59C LEU* 6.4 0.4 - - - +
86C ILE* 3.6 20.5 - - + +
89C HIS* 3.3 30.8 - - + +
106C PRO* 3.0 26.8 + - + +
107C GLN* 4.1 2.0 - - - +
109C ILE* 1.3 87.6 - - + +
111C HIS* 1.3 57.0 - - - +
112C GLY 3.2 1.0 + - - -
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Residues in contact with HIS 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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89C HIS* 3.0 21.1 + - - +
92C LEU* 4.4 11.4 - - + -
93C GLU 3.2 27.8 - - - -
94C LYS* 3.4 16.6 + - - +
96C ASP 3.0 21.6 + - - -
98C ILE* 3.5 16.1 - - + +
107C GLN 3.2 16.7 + - - +
108C ILE 3.8 6.3 - - - +
109C ILE 3.0 1.6 - - - -
110C TRP* 1.3 76.8 - - - +
112C GLY* 1.3 55.2 + - - +
113C LEU 3.9 0.2 - - - -
135C VAL* 3.5 12.2 - - - +
136C ASN 3.8 12.3 - - - -
137C VAL* 3.7 23.3 - - + -
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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