Contacts of the helix formed by residues 128 - 143 (chain B) in PDB entry 3N3B
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 128 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B TRP* 3.1 49.0 + - + +
125B SER* 3.7 9.0 - - - +
126B GLU 3.4 2.0 - - - -
127B GLU* 1.3 75.9 - - - +
129B ALA* 1.3 64.5 + - - +
130B PRO* 3.4 7.3 - - - +
131B LEU* 3.1 31.6 + - + +
132B GLN* 3.2 25.8 + - - +
236B TYR* 3.2 21.8 - - - -
239B GLU* 2.9 20.7 + - - +
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Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B GLU 3.5 6.1 + - - +
128B ASN* 1.3 70.5 - - - +
130B PRO* 1.4 68.3 - - + +
132B GLN* 3.3 5.4 + - - +
133B ARG* 2.9 32.7 + - - +
239B GLU* 4.8 1.7 + - - +
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Residues in contact with PRO 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ASN* 3.4 10.3 - - - +
129B ALA* 1.4 94.8 - - + +
131B LEU* 1.3 55.7 + - - +
134B LYS* 3.0 17.8 + - - +
232B ASN* 2.8 42.9 - - - +
235B GLN* 3.9 18.6 - - + -
236B TYR* 3.7 27.5 - - + +
239B GLU* 3.4 28.9 - - - +
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Residues in contact with LEU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B GLY* 3.9 27.6 - - - +
65B LEU* 4.2 13.9 - - + -
66B LEU* 4.5 9.2 - - + -
124B TRP* 5.7 0.4 - - + -
125B SER* 3.6 41.1 - - - +
128B ASN* 3.1 24.2 - - + +
129B ALA 3.3 0.2 - - - -
130B PRO* 1.3 76.3 - - - +
132B GLN* 1.3 59.7 + - - +
134B LYS* 3.5 26.9 + - - +
135B ALA* 3.1 25.6 + - - +
236B TYR* 3.7 26.4 - - + +
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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
----------------------------------------------------------
5A ARG 6.1 0.8 - - - +
6A ILE 5.5 3.2 + - - -
65B LEU* 3.7 25.8 - - - +
125B SER 3.1 18.2 - - - +
126B GLU* 3.6 36.2 + - - +
128B ASN 3.2 18.1 + - - +
129B ALA* 3.9 4.5 - - - +
131B LEU* 1.3 72.9 - - - +
133B ARG* 1.3 60.1 + - - +
135B ALA* 3.3 7.8 + - - +
136B GLN* 2.9 43.6 + - - +
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Residues in contact with ARG 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ALA 2.9 18.9 + - - +
130B PRO 3.9 3.8 - - - +
132B GLN* 1.3 73.1 - - - +
134B LYS* 1.3 64.5 + - - +
136B GLN* 3.4 23.5 + - - +
137B ILE* 3.1 56.7 + - + +
140B GLN* 5.0 10.7 - - - +
228B GLU* 3.7 20.0 + - - -
232B ASN* 4.0 18.6 - - + +
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Residues in contact with LYS 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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66B LEU* 3.8 34.9 - - + +
130B PRO 3.0 16.3 + - - +
131B LEU* 3.6 18.8 - - - +
132B GLN 3.3 0.2 - - - -
133B ARG* 1.3 78.1 - - - +
135B ALA* 1.3 61.0 + - - +
137B ILE* 4.0 1.7 - - - +
138B ILE* 3.2 31.9 + - + +
157B LEU* 4.6 3.1 - - + -
161B LEU* 3.8 34.8 + - + +
164B SER* 4.5 0.6 + - - -
229B LEU* 4.7 10.0 - - + +
232B ASN* 3.7 9.3 + - - +
233B GLU* 2.9 41.0 + - - +
236B TYR* 3.6 18.3 - - - -
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Residues in contact with ALA 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B LEU* 4.3 20.6 - - + -
66B LEU* 4.6 11.2 - - + -
69B LEU* 4.2 14.1 - - + +
131B LEU 3.1 17.0 + - - +
132B GLN* 3.3 12.8 + - - +
134B LYS* 1.3 78.3 - - - +
136B GLN* 1.3 61.3 + - + +
138B ILE* 3.8 1.4 + - - +
139B GLN* 3.2 27.9 + - - +
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Residues in contact with GLN 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 30.1 + - - +
133B ARG* 3.8 24.1 + - - +
134B LYS 3.3 0.4 - - - -
135B ALA* 1.3 76.1 - - + +
137B ILE* 1.3 60.3 + - - +
139B GLN* 3.8 7.1 - - - +
140B GLN* 2.9 32.5 + - - +
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Residues in contact with ILE 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ARG* 3.1 54.7 + - + +
134B LYS* 4.0 4.5 - - - +
136B GLN* 1.3 74.8 - - - +
138B ILE* 1.3 63.4 + - + +
140B GLN* 3.4 19.4 - - - +
141B HIS* 3.1 29.6 - - + +
225B LEU* 3.8 29.4 - - + -
228B GLU* 3.5 31.9 - - + +
229B LEU* 3.9 20.4 - - + -
232B ASN* 5.6 4.0 - - + +
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Residues in contact with ILE 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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69B LEU* 4.1 13.9 - - + -
134B LYS* 3.2 20.7 + - + +
135B ALA* 4.2 2.9 - - - +
137B ILE* 1.3 79.7 - - + +
139B GLN* 1.3 61.4 + - - +
141B HIS* 3.6 4.0 + - + +
142B TYR* 3.3 51.1 + - + +
153B ALA* 4.0 29.4 - - + +
157B LEU* 4.1 23.6 - - + -
161B LEU* 4.4 6.1 - - + -
225B LEU* 5.7 0.9 - - + -
229B LEU* 3.9 33.7 - - + -
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Residues in contact with GLN 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ARG* 3.6 32.5 - - - +
6A ILE* 4.1 9.3 - - - +
69B LEU* 3.9 12.6 - - + +
73B ILE* 3.5 30.0 - - + +
135B ALA* 3.2 21.3 + - - +
136B GLN* 4.0 6.7 - - - +
137B ILE 3.4 0.2 - - - -
138B ILE* 1.3 74.1 - - - +
140B GLN* 1.3 65.6 + - - +
142B TYR* 3.2 7.9 + - - +
143B ARG* 2.9 52.8 + - - +
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Residues in contact with GLN 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ARG* 5.0 10.7 - - - +
136B GLN 2.9 17.1 + - - +
137B ILE* 3.4 22.1 - - - +
138B ILE 3.3 0.2 - - - -
139B GLN* 1.3 76.7 - - - +
141B HIS* 1.3 77.2 + - - +
143B ARG* 3.6 4.1 + - - +
144B GLY* 3.3 18.0 + - - -
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Residues in contact with HIS 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ILE* 3.1 30.0 + - + +
138B ILE* 3.6 5.6 + - + +
139B GLN 3.3 0.4 - - - -
140B GLN* 1.3 89.8 + - + +
142B TYR* 1.3 64.7 + - - +
144B GLY* 3.3 12.0 + - - +
146B ASP 4.6 2.1 - - - +
149B LYS* 4.3 28.4 - - + +
150B LYS* 3.3 18.9 + - - +
153B ALA* 4.3 9.4 - - + -
221B PHE* 3.4 34.3 - + - -
225B LEU* 3.7 28.8 - - + +
228B GLU* 5.6 0.4 + - - -
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Residues in contact with TYR 142 (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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69B LEU* 4.5 8.7 - - + -
70B GLN* 2.6 31.6 + - - -
73B ILE* 3.7 21.7 - - + +
74B GLY* 3.6 19.7 - - - -
77B SER* 3.6 25.2 - - - +
78B LEU* 5.2 0.9 - - + -
138B ILE* 3.3 39.7 + - + +
139B GLN* 3.2 12.0 + - - +
141B HIS* 1.3 77.7 - - - +
143B ARG* 1.3 58.8 + - - +
144B GLY 3.2 0.4 - - - -
150B LYS* 3.1 59.1 + - + +
153B ALA* 4.4 3.6 - - + -
154B SER* 3.3 26.1 + - - -
157B LEU* 4.5 0.3 - - - +
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Residues in contact with ARG 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ARG* 4.2 26.7 - - - +
6A ILE* 5.2 1.6 - - - +
73B ILE* 3.5 32.1 - - + +
139B GLN* 2.9 44.1 + - + +
140B GLN* 3.8 4.7 - - - +
142B TYR* 1.3 74.6 - - - +
144B GLY* 1.3 63.5 + - - +
150B LYS* 5.1 0.2 - - - +
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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