Contacts of the helix formed by residues 128 - 144 (chain I) in PDB entry 3PB1
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 GLU 128 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125I ASP* 3.5 28.6 + - + +
126I PHE 3.1 2.8 - - - -
127I SER* 1.3 78.9 + - - +
129I VAL* 1.3 58.4 + - - +
130I GLU* 3.4 5.6 - - - -
131I ARG* 3.1 22.3 + - + -
132I ALA* 2.8 27.7 + - - +
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Residues in contact with VAL 129 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126I PHE 3.3 9.4 - - - +
127I SER 3.4 2.6 + - - +
128I GLU* 1.3 73.7 - - - +
130I GLU* 1.3 77.9 + - - +
132I ALA* 3.2 6.8 + - - +
133I ARG* 3.1 59.3 + - - +
157I VAL* 4.2 3.4 - - + +
158I GLN* 3.5 11.2 - - - +
159I GLN* 3.3 42.0 - - + +
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Residues in contact with GLU 130 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128I GLU* 4.6 2.4 - - - -
129I VAL* 1.3 94.5 + - + +
131I ARG* 1.3 59.9 + - - +
133I ARG* 3.5 16.6 + - - +
134I PHE* 3.1 22.0 + - - +
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Residues in contact with ARG 131 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125I ASP 5.8 0.7 - - - +
128I GLU* 3.1 26.4 + - + +
130I GLU* 1.3 75.5 - - - +
132I ALA* 1.3 61.1 + - - +
134I PHE* 3.2 40.3 + - - +
135I ILE* 2.8 50.9 + - + +
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Residues in contact with ALA 132 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124I VAL* 4.7 5.1 - - + +
125I ASP 4.0 11.8 + - - +
126I PHE* 3.8 33.0 - - + -
128I GLU 2.8 13.5 + - - +
129I VAL 3.5 8.7 - - - +
131I ARG* 1.3 76.6 - - - +
133I ARG* 1.3 61.7 + - - +
135I ILE* 3.4 9.5 + - - +
136I ILE* 3.0 31.8 + - - +
157I VAL* 4.2 6.7 - - + -
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Residues in contact with ARG 133 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129I VAL* 3.1 40.1 + - - +
130I GLU* 3.7 17.1 + - - +
132I ALA* 1.3 75.8 - - - +
134I PHE* 1.3 63.9 + - - +
136I ILE* 3.5 4.6 + - - +
137I ASN* 3.0 40.2 + - - +
150I HIS* 5.8 1.1 - - + -
154I THR* 2.9 33.6 + - - +
155I GLY* 3.1 22.2 + - - -
157I VAL* 2.9 31.6 + - + +
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Residues in contact with PHE 134 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130I GLU 3.1 11.3 + - - +
131I ARG* 3.4 44.9 - - - +
133I ARG* 1.3 79.8 - - - +
135I ILE* 1.3 58.8 + - + +
137I ASN* 3.7 3.1 - - - +
138I ASP* 2.8 60.6 + - + +
141I LYS* 6.0 2.9 - - - -
150I HIS* 5.8 3.4 - - - -
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Residues in contact with ILE 135 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98I PHE* 4.4 7.9 - - + -
101I ARG* 5.7 5.2 - - - +
122I LYS* 6.2 0.2 - - + -
124I VAL* 4.0 33.7 - - + -
125I ASP 5.6 2.9 - - - +
131I ARG* 2.8 55.6 + - + +
132I ALA* 3.7 8.1 - - - +
134I PHE* 1.3 82.4 - - + +
136I ILE* 1.3 63.1 + - - +
138I ASP* 3.3 4.8 + - - +
139I TRP* 3.0 23.1 + - + +
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Residues in contact with ILE 136 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98I PHE* 3.8 47.6 - - + -
124I VAL* 5.3 1.8 - - + -
126I PHE* 4.0 26.2 - - + -
132I ALA* 3.0 21.9 + - + +
133I ARG 4.0 2.7 - - - +
135I ILE* 1.3 74.6 - - + +
137I ASN* 1.3 63.8 + - - +
139I TRP* 3.3 6.2 + - - +
140I VAL* 3.3 20.1 + - - +
151I LEU* 4.6 3.8 - - + -
154I THR* 3.9 21.5 - - + -
157I VAL* 4.3 17.3 - - + -
164I VAL* 4.4 9.0 - - + -
166I VAL* 4.0 17.5 - - + -
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Residues in contact with ASN 137 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133I ARG* 3.0 29.2 + - - +
134I PHE* 4.0 2.2 - - - +
136I ILE* 1.3 74.7 - - - +
138I ASP* 1.3 60.0 + - - +
140I VAL* 3.3 5.7 + - - +
141I LYS* 2.9 25.1 + - - +
149I SER 3.5 13.1 - - - +
150I HIS* 3.4 39.3 + - + +
151I LEU* 2.8 38.1 + - - +
154I THR* 3.1 26.0 + - - -
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Residues in contact with ASP 138 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134I PHE* 2.8 49.6 + - + +
135I ILE* 3.6 6.5 - - - +
137I ASN* 1.3 69.9 - - - +
139I TRP* 1.3 64.4 + - - +
141I LYS* 3.3 22.5 + - - +
142I THR* 2.9 44.6 + - - +
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Residues in contact with TRP 139 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94I THR* 2.8 28.1 + - + -
95I ASP 4.2 5.4 - - - -
96I ALA* 3.7 19.2 - - + +
98I PHE* 4.0 13.9 - + + -
119I SER* 6.4 0.2 - - - -
122I LYS* 3.2 49.1 - - + -
135I ILE* 3.0 12.4 + - + +
136I ILE 3.4 9.4 - - - +
137I ASN 3.3 0.2 - - - -
138I ASP* 1.3 77.3 - - - +
140I VAL* 1.3 69.0 + - + +
142I THR* 4.7 1.1 - - - -
143I HIS* 2.9 71.4 + + - +
166I VAL* 6.1 1.1 - - + -
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Residues in contact with VAL 140 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94I THR* 4.6 5.8 - - + -
98I PHE* 6.3 0.2 - - + -
136I ILE* 3.3 12.9 + - + +
137I ASN* 3.3 10.5 + - - +
139I TRP* 1.3 84.6 - - + +
141I LYS* 1.3 59.1 + - - +
143I HIS 3.9 0.2 - - - -
144I THR* 2.9 30.7 + - - +
148I ILE* 3.5 34.8 - - + +
149I SER 5.0 3.1 - - - -
151I LEU* 4.4 17.7 - - + -
166I VAL* 3.6 30.7 - - + -
168I ALA* 3.9 16.6 - - + -
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Residues in contact with LYS 141 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134I PHE* 6.0 3.4 - - - -
137I ASN 2.9 16.4 + - - +
138I ASP* 3.6 22.7 + - - +
140I VAL* 1.3 77.3 - - - +
142I THR* 1.3 63.7 + - + +
144I THR* 3.5 0.5 + - - -
145I LYS 3.3 2.6 + - - -
146I GLY* 2.7 42.9 + - - +
148I ILE 3.2 10.0 + - - +
149I SER* 3.9 31.1 + - - +
150I HIS* 5.0 9.7 + - - -
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Residues in contact with THR 142 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138I ASP* 2.9 36.2 + - - +
139I TRP* 4.5 2.7 - - - +
141I LYS* 1.3 77.6 - - + +
143I HIS* 1.3 78.5 + - + +
145I LYS* 2.9 25.6 + - - +
146I GLY 4.9 0.2 - - - +
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Residues in contact with HIS 143 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92I SER* 3.9 12.3 + - - -
93I THR 4.1 10.4 + - - +
94I THR* 3.5 26.8 - - + +
139I TRP* 2.9 74.1 + + - +
142I THR* 1.3 93.6 + - + +
144I THR* 1.3 60.5 + - - +
145I LYS* 3.4 5.5 - - - +
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Residues in contact with THR 144 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92I SER* 3.9 17.5 + - - -
94I THR* 4.4 2.9 - - + -
140I VAL 2.9 23.1 + - - +
141I LYS 3.5 2.6 + - - -
142I THR 3.2 0.4 - - - -
143I HIS* 1.3 79.2 - - - +
145I LYS* 1.3 70.6 + - - +
146I GLY 3.2 0.2 - - - -
147I MET* 3.0 22.1 + - - +
148I ILE* 2.9 40.7 + - + -
168I ALA* 4.0 36.3 - - + +
169I LEU* 4.6 2.2 - - - +
170I TYR* 4.9 1.3 - - - -
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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