Contacts of the helix formed by residues 104 - 111 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A GLN* 3.3 5.9 + - - -
100A PRO* 3.5 30.2 - - + +
101A GLY* 2.9 28.8 + - - +
103A ARG* 1.3 79.6 + - - +
105A VAL* 1.3 63.8 + - - +
107A GLN* 3.0 40.2 + - - +
108A ILE* 3.9 3.1 + - - +
140A PRO* 5.6 0.2 - - - -
170A TYR* 3.3 22.8 - - + +
171A THR* 5.2 0.9 - - - -
200A GLN* 3.0 25.2 + - - -
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Residues in contact with VAL 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A LEU* 6.0 1.1 - - + -
75A TYR* 5.9 11.9 - - + -
76A ALA 6.2 0.2 - - - +
78A THR* 6.0 0.4 - - + -
102A TYR 3.8 19.7 - - - +
103A ARG* 3.3 2.0 - - - -
104A ASP* 1.3 75.3 - - - +
106A PRO* 1.3 75.0 - - + +
107A GLN 3.1 0.9 + - - -
108A ILE* 3.1 19.3 - - + +
109A ILE* 3.1 37.2 + - + +
118A ALA* 3.8 21.1 - - + +
121A PHE* 4.5 11.2 - - + -
140A PRO* 4.2 16.8 - - + -
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Residues in contact with PRO 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A THR* 3.8 28.0 - - + +
59A LEU* 4.8 10.3 - - + -
78A THR* 3.8 14.4 - - + +
85A GLN* 3.4 15.3 - - - +
86A ILE* 3.9 12.3 - - + -
103A ARG 3.7 10.1 - - - +
104A ASP 3.5 4.0 - - - -
105A VAL* 1.3 94.5 - - + +
107A GLN* 1.3 66.6 + - - +
109A ILE* 3.3 11.5 + - + +
110A TRP* 2.9 32.8 + - + +
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Residues in contact with GLN 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A GLN* 3.4 49.2 - - - +
86A ILE* 4.9 0.6 - - - +
89A HIS* 3.7 16.2 - - + -
98A ILE* 4.4 20.0 - - + -
104A ASP* 3.0 49.6 + - + +
105A VAL 3.1 0.4 + - - -
106A PRO* 1.3 76.7 - - - +
108A ILE* 1.3 59.0 + - - +
109A ILE 3.3 0.2 + - - -
110A TRP* 3.3 2.4 + - - -
111A HIS* 3.0 27.8 + - - +
170A TYR* 3.5 33.7 - - + +
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Residues in contact with ILE 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A ILE* 4.3 6.3 - - + -
100A PRO* 3.5 30.3 - - + -
104A ASP 3.9 0.2 + - - -
105A VAL* 3.1 21.8 - - + +
107A GLN* 1.3 76.5 - - - +
109A ILE* 1.3 58.8 + - - +
110A TRP 3.4 0.2 - - - -
111A HIS* 3.4 7.9 + - - +
112A GLY 3.4 5.5 + - - -
113A LEU* 2.9 51.1 + - + +
131A ILE* 5.8 0.9 - - + -
137A VAL* 3.7 32.0 - - + +
138A LEU 4.3 4.9 - - - +
139A PRO* 4.9 1.3 - - + -
140A PRO* 3.9 33.9 - - + -
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Residues in contact with ILE 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A TYR* 5.9 5.4 - - + -
59A LEU* 3.9 20.6 - - + -
105A VAL* 3.1 24.3 + - + +
106A PRO* 3.5 7.6 - - + +
108A ILE* 1.3 79.1 - - + +
110A TRP* 1.3 74.7 + - + +
112A GLY* 3.2 11.3 + - - -
113A LEU* 3.4 24.2 + - + +
115A LEU* 3.8 36.3 - - + +
118A ALA* 3.8 25.8 - - + -
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Residues in contact with TRP 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A GLU* 4.7 5.8 - - - -
51A ARG* 5.1 0.9 - - + -
52A ARG* 3.7 64.4 + - + +
55A TYR* 3.5 48.9 - + + -
56A THR* 3.1 18.5 + - - -
59A LEU* 6.0 2.0 - - - +
86A ILE* 3.6 19.7 - - + +
89A HIS* 3.4 28.9 - - + +
106A PRO* 2.9 27.5 + - + +
107A GLN* 3.9 2.2 - - - +
109A ILE* 1.3 86.2 - - + +
111A HIS* 1.3 58.9 + - - +
112A GLY 3.2 1.5 + - - -
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Residues in contact with HIS 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A HIS* 3.0 27.1 + + - +
92A LEU* 4.5 8.3 - - + -
93A GLU 3.3 26.9 - - - -
94A LYS* 3.6 12.9 + - - +
96A ASP 2.8 23.6 + - - -
98A ILE* 3.4 18.1 - - + +
107A GLN 3.0 13.3 + - - +
108A ILE 3.8 6.5 - - - +
109A ILE 3.1 0.6 - - - -
110A TRP* 1.3 77.1 - - - +
112A GLY* 1.3 55.6 + - - +
113A LEU 3.9 0.2 - - - -
135A VAL* 3.4 14.9 - - - +
136A ASN 3.7 11.9 - - - -
137A VAL* 3.5 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