Contacts of the helix formed by residues 123 - 137 (chain B) in PDB entry 7V3X
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 LEU 123 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122B ASP* 1.3 79.1 - - - +
124B SER* 1.3 61.1 + - - +
126B LEU* 3.8 4.8 + - - +
127B ILE* 3.5 17.5 + - - +
163B GLU* 5.2 13.9 - - + -
166B ARG* 4.6 21.5 - - + +
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Residues in contact with SER 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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122B ASP 5.8 0.3 + - - -
123B LEU* 1.3 75.9 + - - +
125B ALA* 1.3 67.0 + - - +
127B ILE* 3.3 8.7 + - - +
128B GLU* 3.0 24.1 + - - +
166B ARG* 4.4 21.6 + - - +
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Residues in contact with ALA 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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122B ASP* 3.3 20.3 + - + +
124B SER* 1.3 82.4 + - - +
126B LEU* 1.3 61.9 + - - +
128B GLU* 3.4 8.0 + - - +
129B ARG* 3.2 27.6 + - - +
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Residues in contact with LEU 126 (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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74B VAL* 6.4 0.9 - - + -
76B PHE* 6.0 7.4 - - + -
108B ALA* 6.3 2.9 - - + -
122B ASP 3.0 16.6 + - - +
123B LEU* 3.9 5.2 - - - +
125B ALA* 1.3 71.7 - - - +
127B ILE* 1.3 53.1 + - - +
129B ARG* 2.9 19.6 + - - +
130B ILE* 2.7 49.4 + - + +
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Residues in contact with ILE 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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123B LEU 3.5 11.8 + - - +
124B SER* 3.3 13.3 + - - +
126B LEU* 1.3 76.4 - - - +
128B GLU* 1.3 53.0 + - - +
130B ILE* 3.3 12.1 + - - +
131B ASN* 2.6 38.2 + - - +
167B LEU* 6.1 3.6 - - - -
170B ARG* 4.9 17.7 - - + -
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Residues in contact with GLU 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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124B SER 3.0 12.9 + - - +
125B ALA* 3.4 12.8 - - - +
126B LEU 3.2 0.2 - - - -
127B ILE* 1.3 72.7 - - - +
129B ARG* 1.3 54.6 + - + +
131B ASN* 3.6 6.4 - - - +
132B TYR* 2.7 36.1 + - - +
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Residues in contact with ARG 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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106B LEU* 3.0 39.9 - - + +
107B ASP 3.1 20.6 + - - +
108B ALA* 4.2 13.1 - - - +
125B ALA* 3.2 15.0 + - - +
126B LEU* 2.9 15.6 + - - +
128B GLU* 1.3 75.3 - - + +
130B ILE* 1.3 53.5 + - - +
132B TYR* 3.3 10.3 + - - +
133B ALA* 2.9 35.0 + - - +
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Residues in contact with ILE 130 (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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72B VAL* 5.5 2.7 - - + -
74B VAL* 4.1 21.5 - - + -
76B PHE* 6.2 2.0 - - + -
106B LEU* 3.9 21.8 - - + -
126B LEU* 2.7 36.1 + - + +
127B ILE* 3.7 9.0 - - - +
129B ARG* 1.3 67.2 - - - +
131B ASN* 1.3 58.9 + - - +
133B ALA* 3.4 3.8 + - - +
134B ILE* 2.7 51.0 + - + +
142B VAL* 4.5 12.3 - - + -
144B ILE* 4.9 13.2 - - + -
171B LEU* 4.4 17.9 - - + -
174B ILE* 6.5 0.2 - - + -
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Residues in contact with ASN 131 (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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127B ILE 2.6 22.8 + - - +
128B GLU* 3.6 7.9 - - - +
130B ILE* 1.3 71.2 - - - +
132B TYR* 1.3 62.5 + - - +
134B ILE* 3.2 19.2 + - - +
135B GLN* 3.4 12.5 + - - +
174B ILE* 4.6 25.7 - - + +
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Residues in contact with TYR 132 (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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128B GLU 2.7 22.0 + - - +
129B ARG* 3.5 8.5 - - - +
131B ASN* 1.3 72.9 - - - +
133B ALA* 1.3 55.4 + - + +
135B GLN* 3.4 4.7 + - + +
136B LYS* 2.8 52.9 + - + +
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Residues in contact with ALA 133 (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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72B VAL* 4.3 14.0 - - + +
104B PHE* 3.9 31.9 - - + -
106B LEU* 4.6 1.8 - - + -
129B ARG 2.9 18.1 + - - +
130B ILE* 3.5 9.0 - - - +
132B TYR* 1.3 79.0 - - + +
134B ILE* 1.3 58.0 - - - +
136B LYS* 3.2 6.2 + - - -
137B TYR* 3.0 37.9 + - - +
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Residues in contact with ILE 134 (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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72B VAL* 4.8 6.3 - - + -
130B ILE* 2.7 39.5 + - + +
131B ASN* 3.2 7.8 + - - +
133B ALA* 1.3 75.5 - - + +
135B GLN* 1.3 53.3 + - - +
138B ARG* 2.8 30.0 + - - -
139B ALA* 2.9 37.9 + - + +
142B VAL* 3.8 28.7 - - + -
171B LEU* 4.5 5.2 - - + -
174B ILE* 3.8 32.3 - - + +
176B ALA* 4.2 8.7 - - + -
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Residues in contact with GLN 135 (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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131B ASN 3.4 7.5 + - - +
132B TYR* 4.0 6.7 - - + +
134B ILE* 1.3 73.9 - - - +
136B LYS* 1.3 58.0 - - - +
137B TYR 3.1 10.3 + - - -
138B ARG* 3.4 15.6 + - - +
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Residues in contact with LYS 136 (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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132B TYR* 2.8 44.5 + - + +
133B ALA* 3.2 8.9 + - - +
135B GLN* 1.3 74.3 - - - +
137B TYR* 1.3 74.3 + - + +
138B ARG* 5.6 0.4 - - - -
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Residues in contact with TYR 137 (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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70B PRO* 3.4 18.6 - - + +
71B GLY 5.8 0.9 - - - +
72B VAL* 5.2 2.7 - - + -
98B VAL* 5.4 3.0 + - + +
101B GLY* 3.3 30.7 - - - +
102B LYS 5.2 0.9 - - - +
103B LEU 3.7 21.1 - - - -
104B PHE* 3.5 44.8 - + + -
133B ALA* 3.0 19.3 + - - +
134B ILE 4.4 0.9 - - - +
136B LYS* 1.3 100.5 - - + +
138B ARG* 1.3 74.2 + - - +
139B ALA* 3.1 10.4 + - + -
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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