Contacts of the helix formed by residues 130 - 141 (chain B) in PDB entry 3SEA
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 SER 130 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85B TYR* 4.6 1.2 + - - -
127B ARG* 3.9 6.1 - - - +
128B VAL 4.3 0.2 - - - -
129B ILE* 1.3 78.6 - - - +
131B TYR* 1.3 65.7 + - - +
132B GLU* 3.4 8.8 + - - +
133B GLU* 2.9 47.8 + - - +
134B GLY* 3.4 8.3 + - - -
147B GLU* 4.2 1.9 - - - +
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Residues in contact with TYR 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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124A HIS 6.1 0.7 - - - -
127A ARG* 3.4 34.5 - - + -
130A SER* 3.7 19.6 - - - -
131A TYR* 2.9 37.9 + - - +
132A GLU 4.4 0.9 + - - -
127B ARG* 3.8 6.6 - - - +
130B SER* 1.3 73.2 - - - +
132B GLU* 1.3 68.8 + - + +
134B GLY 3.3 2.4 + - - -
135B LYS* 3.0 35.9 + - + +
145B PHE* 3.5 29.5 + + - -
146B LEU* 5.4 1.8 - - - -
147B GLU* 3.5 39.9 - - + +
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Residues in contact with GLU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LYS 5.2 2.8 - - - +
124A HIS* 3.4 55.3 - - + +
127A ARG* 4.9 6.9 + - - -
130B SER* 3.2 7.6 + - - +
131B TYR* 1.3 82.8 - - + +
133B GLU* 1.3 58.4 + - + +
135B LYS* 4.1 17.8 - - - +
136B ALA* 2.8 46.4 + - + +
139B GLU* 5.5 2.9 - - - +
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Residues in contact with GLU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B PHE* 3.5 19.0 - - + -
128B VAL 4.4 2.9 - - - +
129B ILE* 3.6 18.7 - - + +
130B SER* 2.9 43.1 + - - +
132B GLU* 1.3 77.5 - - + +
134B GLY* 1.3 59.4 + - - +
136B ALA* 4.1 4.0 - - - +
137B LEU* 3.3 16.1 + - - +
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Residues in contact with GLY 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B TYR* 3.5 22.6 + - - -
93B PHE* 4.0 9.3 - - - -
116B LEU* 3.2 11.1 - - - +
130B SER 3.4 5.3 + - - -
131B TYR 3.3 2.8 + - - -
132B GLU 3.2 0.4 - - - -
133B GLU* 1.3 76.6 - - - +
135B LYS* 1.3 59.5 + - - +
137B LEU 3.2 1.4 + - - -
138B ALA* 2.8 26.2 + - - +
145B PHE* 3.6 13.2 - - - -
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Residues in contact with LYS 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LYS* 5.9 2.5 - - - -
127A ARG* 3.4 26.0 - - - +
131A TYR* 3.0 40.0 - - - +
147A GLU* 3.6 5.6 - - - -
131B TYR* 3.0 39.3 + - + +
132B GLU* 3.9 15.3 - - - +
134B GLY* 1.3 73.9 - - - +
136B ALA* 1.3 58.6 + - - +
138B ALA* 3.2 2.3 + - + +
139B GLU* 2.8 59.4 + - + +
145B PHE* 3.5 24.3 - - + +
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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
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132B GLU* 2.8 36.1 + - + +
133B GLU* 4.1 5.2 - - - +
135B LYS* 1.3 73.5 - - - +
137B LEU* 1.3 61.3 + - - +
139B GLU* 3.3 13.0 + - - +
140B SER* 3.1 22.5 + - - -
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Residues in contact with LEU 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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93B PHE* 3.6 24.9 - - + -
96B ILE* 4.3 5.2 - - + -
97B LYS* 3.7 35.2 - - + +
116B LEU* 3.8 13.9 - - + -
133B GLU 3.3 15.8 + - - +
134B GLY 3.2 5.2 + - - +
136B ALA* 1.3 77.3 - - - +
138B ALA* 1.3 65.6 + - - +
140B SER* 2.8 28.6 + - - +
141B TRP* 3.3 50.5 + - + +
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Residues in contact with ALA 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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116B LEU* 3.6 12.7 - - + +
134B GLY 2.8 16.6 + - - +
135B LYS 3.5 3.1 - - - +
137B LEU* 1.3 71.4 - - - +
139B GLU* 1.3 59.1 + - + +
141B TRP* 2.9 20.8 + - - +
143B ALA* 2.9 37.4 + - - +
144B ALA 3.8 5.4 - - - +
145B PHE* 3.3 33.7 - - + -
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Residues in contact with GLU 139 (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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121A LYS* 5.3 11.5 + - - +
132B GLU* 5.5 2.5 - - - +
135B LYS* 2.8 59.9 + - + +
136B ALA* 3.6 10.0 - - - +
138B ALA* 1.3 73.6 - - + +
140B SER* 1.3 56.9 + - - +
141B TRP 3.0 0.2 - - - -
142B ASN* 2.9 20.4 + - - +
143B ALA 4.3 3.6 + - - +
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Residues in contact with SER 140 (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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136B ALA 3.1 10.2 + - - -
137B LEU* 2.8 28.2 + - - +
139B GLU* 1.3 75.8 - - - +
141B TRP* 1.3 69.8 + - - +
142B ASN 3.3 0.4 + - - -
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Residues in contact with TRP 141 (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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83B LEU* 3.9 20.2 - - + -
96B ILE* 3.9 13.9 - - + -
97B LYS* 4.2 7.3 - - - +
100B HIS* 3.4 65.4 + + + +
114B ILE* 4.3 11.1 - - + +
116B LEU* 3.7 31.6 - - + -
137B LEU* 3.4 45.2 - - + +
138B ALA* 2.9 9.7 + - - +
140B SER* 1.3 90.7 + - - +
142B ASN* 1.3 70.8 + - - +
143B ALA* 3.9 20.1 - - + +
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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