Contacts of the helix formed by residues 126 - 138 (chain B) in PDB entry 4P22
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 ASN 126 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B ASP 2.7 28.7 + - - -
104B GLN 3.8 9.7 + - - -
105B GLY 3.8 11.6 + - - -
106B THR* 4.1 7.9 - - + +
124B GLY 3.8 2.0 + - - -
125B LYS* 1.3 69.9 - - - +
127B ARG* 1.3 64.5 + - - +
128B ALA* 2.8 23.6 + - - +
129B GLU* 2.8 28.8 + - + +
130B VAL* 3.0 25.0 + - - +
148B THR* 3.3 25.3 - - + +
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Residues in contact with ARG 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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80B LEU* 3.0 14.7 - - + +
81B ARG* 3.8 21.5 - - - +
103B ASP* 2.8 42.0 + - - +
105B GLY* 3.0 24.6 + - - +
106B THR 3.1 15.0 + - - -
107B ALA* 3.6 21.1 - - + +
108B GLN* 4.6 4.6 - - - +
111B ASP* 2.6 42.3 + - - -
118B LEU* 4.3 14.8 - - + -
125B LYS 4.2 1.1 - - - -
126B ASN* 1.3 71.8 - - - +
128B ALA* 1.3 61.2 + - - +
130B VAL* 4.2 0.5 - - - +
131B SER* 2.9 31.5 + - - -
166B ASN* 3.2 24.5 - - - +
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Residues in contact with ALA 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B LEU* 2.3 31.5 - - + +
101B LEU* 3.7 17.5 - - - +
103B ASP* 3.6 27.6 - - - +
126B ASN* 2.8 9.1 + - - +
127B ARG* 1.3 72.0 - - - +
129B GLU* 1.3 58.1 + - - +
131B SER 3.3 1.4 + - - -
132B GLN* 3.1 29.3 + - - +
146B ALA* 3.9 9.1 - - + +
147B TYR 4.4 2.5 - - - +
148B THR* 4.7 0.7 - - + -
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Residues in contact with GLU 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ASN* 2.8 24.9 + - + +
128B ALA* 1.3 75.3 - - - +
130B VAL* 1.3 64.1 + - + +
132B GLN* 3.6 6.1 + - + +
133B PRO* 3.3 19.2 - - - +
146B ALA* 3.8 21.5 - - + +
147B TYR* 5.7 0.2 - - - -
148B THR* 3.2 29.2 + - - +
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Residues in contact with VAL 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B TYR* 4.9 4.2 - - + +
118B LEU* 3.5 30.3 - - + +
122B ASP* 3.5 33.7 - - + +
125B LYS* 3.4 34.1 - - + +
126B ASN 3.0 20.7 + - - +
129B GLU* 1.3 75.1 - - + +
131B SER* 1.3 62.6 + - - +
132B GLN 3.4 0.7 + - - -
133B PRO* 3.4 10.6 - - - +
134B ARG* 4.6 8.7 - - - +
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Residues in contact with SER 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B LEU* 3.6 18.0 - - - +
85B VAL* 4.9 2.0 - - - -
115B GLN* 2.4 34.5 + - - +
117B TYR* 4.3 8.8 - - - -
118B LEU* 4.0 2.9 - - - +
127B ARG 2.9 20.0 + - - -
128B ALA 3.3 0.2 + - - -
130B VAL* 1.3 79.8 - - - +
132B GLN* 1.3 57.1 + - - +
134B ARG* 3.4 8.1 + - - +
135B LEU* 3.1 41.6 + - - +
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Residues in contact with GLN 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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101B LEU* 3.8 16.2 - - + -
128B ALA 3.1 17.1 + - - +
129B GLU* 3.9 6.3 - - + +
131B SER* 1.3 75.1 - - - +
133B PRO* 1.4 85.8 - - + +
135B LEU* 3.4 1.6 + - - +
136B ALA* 2.9 27.1 + - - +
144B VAL* 2.7 37.0 + - - +
145B THR* 3.3 8.5 - - - +
146B ALA* 4.2 13.0 - - + -
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Residues in contact with PRO 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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129B GLU 3.3 17.0 - - - +
130B VAL 3.4 11.2 - - - +
132B GLN* 1.4 102.2 - - + +
134B ARG* 1.3 69.6 + - + +
136B ALA* 3.3 12.4 + - + +
137B GLU* 3.3 23.6 + - - +
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Residues in contact with ARG 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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117A TYR* 6.3 0.8 - - - -
134A ARG* 6.0 3.2 - - - +
137A GLU* 5.4 5.1 + - - -
117B TYR* 3.1 53.1 + - + +
130B VAL 4.6 8.3 - - - +
131B SER 3.7 5.6 - - - +
132B GLN 3.2 0.4 - - - -
133B PRO* 1.3 80.5 - - + +
135B LEU* 1.3 68.0 + - - +
137B GLU* 3.0 49.8 + - - +
138B LEU* 3.8 4.2 + - - +
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Residues in contact with LEU 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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80B LEU* 5.5 1.3 - - + -
85B VAL* 4.3 8.7 - - + -
88B ALA* 4.1 9.2 - - + -
89B LYS* 3.9 20.9 - - + +
92B ILE* 3.9 21.3 - - + +
101B LEU* 3.6 35.7 - - + -
117B TYR* 3.5 21.3 - - + -
131B SER* 3.1 29.5 + - - +
132B GLN 3.8 4.0 - - - +
134B ARG* 1.3 76.2 - - - +
136B ALA* 1.3 59.6 + - - +
137B GLU 3.3 0.7 + - - -
138B LEU* 3.3 39.8 + - + +
144B VAL* 4.3 7.0 - - + -
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Residues in contact with ALA 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B GLN* 2.9 29.3 + - - +
133B PRO* 3.4 10.8 - - + +
134B ARG 3.1 0.4 - - - -
135B LEU* 1.3 76.3 - - - +
137B GLU* 1.3 61.6 + - + +
138B LEU 3.5 0.2 + - - -
139B ASN 4.1 14.6 - - - +
140B SER* 5.2 1.7 - - - -
142B VAL 5.0 2.6 - - - +
144B VAL* 4.0 22.2 - - + +
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Residues in contact with GLU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ARG* 3.6 37.0 + - - +
133B PRO* 3.4 16.7 - - - +
134B ARG* 3.0 50.3 + - - +
136B ALA* 1.3 78.4 - - + +
138B LEU* 1.3 63.9 + - + +
139B ASN* 3.3 2.5 + - - -
140B SER 5.0 0.9 + - - -
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Residues in contact with LEU 138 (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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116A PHE* 3.7 37.7 - - + +
119A ARG* 4.7 6.0 + - - +
89B LYS* 3.4 45.1 - - + +
92B ILE* 3.9 11.4 - - + -
93B LEU* 4.1 20.0 - - + +
117B TYR* 3.5 18.6 - - - +
134B ARG 4.0 3.4 - - - +
135B LEU* 3.4 26.5 - - + +
136B ALA 3.3 0.6 - - - -
137B GLU* 1.3 78.7 - - + +
139B ASN* 1.3 61.4 + - - +
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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