Contacts of the helix formed by residues 120 - 130 (chain B) in PDB entry 3EB6
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 VAL 120 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B PRO 2.9 11.2 + - - +
78B ILE 3.6 25.4 - - - +
79B ASN* 3.7 18.8 - - + -
80B SER 4.7 2.0 - - - +
118B PRO 4.5 0.9 - - - -
119B LEU* 1.3 78.7 - - + +
121B PRO* 1.4 59.1 - - + +
122B GLU* 3.7 27.4 - - + -
123B ILE* 3.0 39.7 + - + +
124B ALA* 3.2 11.6 + - - +
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Residues in contact with PRO 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B PRO* 4.5 12.3 - - + +
119B LEU 3.3 11.4 - - - +
120B VAL* 1.4 83.5 - - + +
122B GLU* 1.3 68.8 + - + +
123B ILE 3.4 0.3 + - - -
124B ALA* 4.0 8.9 - - + +
125B ARG* 3.3 28.3 + - - +
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Residues in contact with GLU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B TYR* 5.2 0.2 + - - -
120B VAL* 3.7 18.6 - - + -
121B PRO* 1.3 81.6 - - + +
123B ILE* 1.3 60.1 + - + +
125B ARG* 3.2 49.0 + - - +
126B ILE* 3.8 7.8 - - - +
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Residues in contact with ILE 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ILE 5.4 1.3 - - - +
74B TYR* 3.6 51.8 - - + +
75B HIS 3.7 28.9 - - - +
76B PRO* 3.8 24.9 - - + -
78B ILE 4.8 1.8 - - - +
120B VAL* 3.0 31.7 + - + +
122B GLU* 1.3 77.9 - - + +
124B ALA* 1.3 67.3 + - - +
125B ARG 3.3 0.2 - - - -
126B ILE* 3.2 6.9 + - - +
127B TYR* 3.1 17.8 + - - +
134B TYR* 4.0 7.2 - - + -
141B TRP* 6.2 0.9 - - + -
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Residues in contact with ALA 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B PRO* 3.9 15.2 - - + +
114B ASN 5.0 4.0 - - - +
118B PRO* 3.6 38.4 - - + -
120B VAL 3.2 6.8 + - - +
121B PRO* 3.6 5.6 + - + +
123B ILE* 1.3 78.2 - - - +
125B ARG* 1.3 52.0 + - - +
127B TYR* 3.0 8.1 + - - +
128B LYS* 2.8 43.5 + - + +
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Residues in contact with ARG 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B PRO 3.3 11.0 + - - +
122B GLU* 3.2 56.0 + - - +
124B ALA* 1.3 77.9 - - - +
126B ILE* 1.3 86.2 + - + +
128B LYS* 3.3 23.8 + - - +
129B THR 4.2 2.4 + - - -
130B ASP* 5.4 0.7 - - - +
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Residues in contact with ILE 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B TYR* 4.4 13.7 - - - +
122B GLU 3.8 15.7 - - - +
123B ILE 3.2 6.6 + - - +
125B ARG* 1.3 99.0 - - - +
127B TYR* 1.3 63.0 + - - +
130B ASP* 3.0 39.6 + - + +
133B LYS* 4.1 24.7 - - + -
134B TYR* 3.8 28.3 - - + +
137B ILE* 4.8 2.2 - - + -
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Residues in contact with TYR 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B PRO* 4.9 5.2 - - + -
111B CYS 5.2 0.7 + - - -
112B ASP* 4.7 3.1 + - - -
113B PRO* 3.2 47.7 + - + +
114B ASN 4.9 11.0 - - - -
123B ILE 3.1 11.4 + - - +
124B ALA* 3.0 14.3 + - - +
126B ILE* 1.3 78.1 - - - +
128B LYS* 1.3 67.8 + - + +
129B THR 3.3 0.9 + - - -
130B ASP 3.7 1.9 + - - -
131B ARG* 2.7 77.0 + - - -
134B TYR* 3.6 52.7 - + + +
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Residues in contact with LYS 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B ASN 5.4 0.7 - - - +
115B PRO* 3.3 46.5 + - + +
118B PRO* 6.1 0.4 - - + -
124B ALA* 2.8 38.5 + - + +
125B ARG* 3.3 14.0 + - - +
127B TYR* 1.3 81.7 - - + +
129B THR* 1.3 69.6 + - - +
131B ARG* 3.8 15.0 + - - +
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Residues in contact with THR 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B ARG 4.2 2.2 + - - -
126B ILE 4.2 0.8 + - - -
128B LYS* 1.3 84.4 + - - +
130B ASP* 1.3 63.9 + - - +
131B ARG* 4.0 2.0 - - - +
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Residues in contact with ASP 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ARG 5.4 0.7 - - - +
126B ILE* 3.0 29.7 + - + +
127B TYR 3.7 0.8 + - - -
129B THR* 1.3 80.2 - - - +
131B ARG* 1.3 66.9 + - - +
132B GLU* 3.3 11.2 - - - +
133B LYS* 3.3 40.0 + - + +
134B TYR 3.1 14.9 + - - -
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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