Contacts of the helix formed by residues 139 - 150 (chain B) in PDB entry 3HCD
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 CYS 139 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A CYS* 2.0 57.8 + - - -
129A HIS* 3.6 25.6 - - + +
132A LEU* 4.7 1.8 - - - -
128B GLN* 5.5 0.9 - - - +
131B CYS* 3.7 1.6 - - - -
137B GLY 3.6 1.8 + - - -
138B GLU* 1.3 83.3 - - - +
140B TRP* 1.3 67.1 + - + +
141B GLN* 3.9 4.9 - - - +
142B ASP* 3.2 28.7 + - - -
143B LYS 3.1 16.1 + - - -
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Residues in contact with TRP 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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125A MET* 3.3 12.2 - - + +
128A GLN* 3.1 34.4 + - - +
124B SER* 3.7 30.3 - - - -
127B SER* 3.6 17.9 - - - -
128B GLN* 3.6 30.7 - - + +
131B CYS* 3.9 9.3 - - - -
138B GLU 4.0 0.2 + - - -
139B CYS* 1.3 72.3 - - + +
141B GLN* 1.3 104.3 - - + +
143B LYS* 3.0 3.7 + - - +
144B GLU* 2.8 57.1 + - - +
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Residues in contact with GLN 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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48A CYS* 3.7 23.5 - - - -
125A MET* 2.6 34.7 - - - +
139B CYS* 3.9 2.1 - - - +
140B TRP* 1.3 117.7 + - + +
142B ASP* 1.3 58.7 + - - +
144B GLU* 3.6 4.4 + - - +
145B ARG* 3.0 44.9 + - - +
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Residues in contact with ASP 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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48A CYS* 4.0 16.6 - - - +
138B GLU* 3.7 18.1 - - + +
139B CYS* 3.2 31.4 + - - +
140B TRP 3.1 0.8 - - - -
141B GLN* 1.3 74.0 - - - +
143B LYS* 1.3 67.0 + - - +
145B ARG* 2.7 36.2 + - - +
146B GLN* 3.0 25.5 + - - +
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Residues in contact with LYS 143 (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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88B LEU* 3.1 43.8 + - + +
89B SER* 4.4 1.2 - - - +
91B CYS* 4.2 7.7 - - - -
92B SER* 4.6 13.5 + - - -
127B SER* 4.5 9.0 - - - +
130B ALA* 4.5 5.4 - - - -
131B CYS* 3.7 28.0 - - - -
134B GLU* 2.7 40.6 + - - -
138B GLU* 3.5 21.6 + - - +
139B CYS 3.1 2.6 + - - -
140B TRP* 3.0 10.2 + - - +
142B ASP* 1.3 79.8 - - - +
144B GLU* 1.3 62.9 + - - +
146B GLN* 3.3 6.4 + - - +
147B LEU* 3.1 20.1 + - - +
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Residues in contact with GLU 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B LEU* 5.3 2.0 - - + -
113B TRP* 4.0 19.8 + - + -
123B TRP* 3.8 6.6 + - - +
124B SER* 3.6 19.2 + - - -
127B SER* 2.6 32.9 + - - +
140B TRP* 2.8 40.4 + - - +
141B GLN* 4.1 4.9 - - - +
143B LYS* 1.3 73.2 - - + +
145B ARG* 1.3 57.2 + - - +
147B LEU* 3.2 8.0 + - - +
148B ARG* 2.9 62.5 + - - +
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Residues in contact with ARG 145 (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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48A CYS* 5.8 0.8 - - - -
141B GLN* 3.0 36.0 + - - +
142B ASP* 2.7 36.1 + - - +
144B GLU* 1.3 72.9 - - - +
146B GLN* 1.3 67.6 + - - +
148B ARG* 4.0 10.2 - - - +
149B ALA* 3.1 25.5 + - + +
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Residues in contact with GLN 146 (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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91B CYS* 4.0 16.6 - - - +
92B SER* 3.7 24.9 + - - +
138B GLU* 4.2 13.0 - - - +
142B ASP 3.0 16.7 + - - +
143B LYS* 3.6 6.1 + - - +
145B ARG* 1.3 77.8 - - - +
147B LEU* 1.3 57.6 + - - +
149B ALA* 3.2 4.9 + - - +
150B ARG* 2.8 68.9 + - + +
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Residues in contact with LEU 147 (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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84B VAL* 4.1 23.1 - - + +
87B LEU* 3.9 20.6 - - + +
88B LEU* 3.7 27.8 - - + -
91B CYS* 3.6 27.1 - - + -
97B ILE* 4.3 4.7 - - + -
99B MET* 6.2 0.4 - - - -
113B TRP* 3.8 23.8 - - + -
143B LYS 3.1 13.5 + - - +
144B GLU* 3.2 8.9 + - - +
146B GLN* 1.3 74.6 - - - +
148B ARG* 1.3 66.3 + - - +
150B ARG 3.8 0.2 - - - -
151B VAL* 2.9 45.1 + - + +
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Residues in contact with ARG 148 (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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113B TRP* 2.9 70.0 + - + +
114B LEU* 3.7 33.2 + - + +
116B GLU* 3.8 41.0 + - - +
144B GLU* 2.9 51.7 + - - +
145B ARG* 4.0 8.1 - - - +
147B LEU* 1.3 76.3 - - - +
149B ALA* 1.3 62.0 + - - +
151B VAL* 3.7 14.7 - - - +
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Residues in contact with ALA 149 (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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145B ARG* 3.1 20.2 + - + +
146B GLN* 3.5 7.6 - - - +
147B LEU 3.1 0.4 - - - -
148B ARG* 1.3 80.3 - - - +
150B ARG* 1.3 65.0 + - + +
151B VAL 4.1 1.7 - - - +
152B LYS* 3.3 21.9 + - - +
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Residues in contact with ARG 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B CYS* 2.9 29.5 + - + -
92B SER 3.8 9.3 + - - -
93B HIS 4.3 0.6 - - - -
94B PHE 3.0 32.9 + - - +
95B GLU* 3.4 35.3 - - - +
97B ILE* 3.0 36.2 + - + -
146B GLN* 2.8 47.5 + - + +
147B LEU 4.2 1.8 - - - +
149B ALA* 1.3 74.7 - - + +
151B VAL* 1.3 58.8 + - - +
152B LYS* 3.0 13.3 + - - +
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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