Contacts of the helix formed by residues 134 - 146 (chain B) in PDB entry 2RCY
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 134 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108B LYS* 3.6 20.6 - - - +
132B ASN 3.3 5.7 + - - +
133B VAL* 1.3 75.8 - - - +
135B SER* 1.3 59.3 + - - +
136B THR* 2.6 29.0 + - + +
137B ASP* 3.0 24.8 + - - +
138B LYS* 2.9 29.9 + - - +
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Residues in contact with SER 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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134B ASN* 1.3 75.5 - - - +
136B THR* 1.3 65.6 + - - +
138B LYS* 3.7 13.3 - - - +
139B LYS* 2.9 29.1 + - - +
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Residues in contact with THR 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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134B ASN* 2.6 26.1 + - - -
135B SER* 1.3 81.4 + - - +
137B ASP* 1.3 65.2 + - - +
139B LYS* 3.6 7.4 - - - +
140B TYR* 3.2 33.3 + - - -
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Residues in contact with ASP 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B LEU* 3.7 26.7 - - + +
108B LYS* 2.8 39.1 + - - +
133B VAL* 3.7 15.6 - - + -
134B ASN* 3.0 29.0 + - - +
136B THR* 1.3 78.0 + - - +
138B LYS* 1.3 58.8 + - - +
139B LYS 3.2 0.2 - - - -
140B TYR* 3.3 12.0 + - - +
141B VAL* 3.1 31.7 + - - +
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Residues in contact with LYS 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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127B TYR* 4.0 17.9 - - + +
129B SER* 3.4 16.6 + - - -
130B ASN 5.8 0.2 - - - -
133B VAL* 3.8 24.7 + - + -
134B ASN 2.9 17.5 + - - +
135B SER* 3.7 12.1 - - - +
136B THR 3.4 0.2 - - - -
137B ASP* 1.3 72.7 - - - +
139B LYS* 1.3 60.7 + - - +
141B VAL* 3.7 7.9 - - - +
142B ASN* 2.9 39.0 + - - +
153B GLU* 3.2 33.6 + - - +
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Residues in contact with LYS 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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135B SER 2.9 18.6 + - - +
136B THR* 3.6 11.2 - - - +
137B ASP 3.2 0.2 - - - -
138B LYS* 1.3 77.2 - - - +
140B TYR* 1.3 61.6 + - + +
142B ASN* 3.6 4.7 + - + +
143B ASP* 3.1 47.6 + - - +
265B GOL 5.2 0.2 - - - -
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Residues in contact with TYR 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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4B ASN 5.4 2.1 + - - -
5B ILE* 3.7 28.6 + - + +
61B ILE* 4.1 27.1 - - + -
86B LEU* 4.9 1.3 - - + -
136B THR* 3.2 24.8 + - - -
137B ASP* 3.3 15.1 + - - +
139B LYS* 1.3 78.0 - - + +
141B VAL* 1.3 59.8 + - - +
143B ASP* 3.3 1.2 + - - +
144B ILE* 2.9 37.3 + - + +
265B GOL 3.5 50.6 + - - -
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Residues in contact with VAL 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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86B LEU* 4.2 12.6 - - + -
88B ILE* 4.8 5.6 - - + -
110B VAL* 4.1 26.2 - - + -
112B VAL* 4.4 4.9 - - + -
127B TYR* 4.2 23.6 - - + -
133B VAL* 5.7 1.3 - - + -
137B ASP 3.1 16.3 + - - +
138B LYS* 3.7 10.3 - - - +
140B TYR* 1.3 75.0 - - - +
142B ASN* 1.3 62.7 + - - +
144B ILE* 4.7 3.4 - - + -
145B PHE* 3.0 46.2 + - + +
151B ILE* 3.9 21.3 - - + +
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Residues in contact with ASN 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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127B TYR* 3.1 28.3 + - - -
138B LYS* 2.9 25.6 + - - +
139B LYS* 4.0 7.6 - - + +
141B VAL* 1.3 76.6 - - - +
143B ASP* 1.3 62.5 + - - +
146B ASN* 2.8 44.1 + - - +
151B ILE* 3.5 28.7 + - - +
153B GLU 5.8 0.6 - - - +
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Residues in contact with ASP 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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28B ILE* 4.0 7.9 - - - +
139B LYS* 3.1 38.5 + - - +
140B TYR 3.9 0.7 - - - +
141B VAL 3.2 0.2 - - - -
142B ASN* 1.3 80.7 - - - +
144B ILE* 1.3 66.2 + - - +
145B PHE 3.4 0.2 - - - -
146B ASN* 4.2 2.3 + - - +
147B SER* 3.6 19.8 + - - -
265B GOL 3.6 23.3 + - - +
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Residues in contact with ILE 144 (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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5B ILE* 5.2 0.9 - - + -
7B LEU* 4.7 9.4 - - + -
23B ILE* 3.8 32.4 - - + +
28B ILE* 3.8 12.8 - - + +
29B ILE* 4.6 9.6 - - + -
61B ILE* 3.9 35.9 - - + -
86B LEU* 6.1 0.2 - - + -
88B ILE* 6.4 0.7 - - + -
140B TYR* 2.9 23.3 + - + +
141B VAL* 3.5 7.4 + - + +
143B ASP* 1.3 77.1 - - - +
145B PHE* 1.3 77.3 + - + +
147B SER* 2.7 22.3 + - - -
148B CYS* 4.2 1.4 - - - -
265B GOL 3.3 20.0 - - - +
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Residues in contact with PHE 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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19B LEU* 3.7 30.7 - - + -
23B ILE* 5.1 1.1 - - + -
63B VAL* 5.6 2.7 - - + -
88B ILE* 3.7 30.1 - - + -
90B ILE* 5.4 0.2 - - + -
112B VAL* 4.0 24.5 - - + -
114B PRO* 5.4 0.7 - - + -
125B PHE* 3.1 54.2 - + + -
141B VAL* 3.0 34.2 + - + +
144B ILE* 1.3 95.0 - - + +
146B ASN* 1.3 64.3 + - - +
147B SER 3.1 2.4 + - - -
148B CYS* 3.4 5.0 + - - -
149B GLY 3.2 9.0 + - - +
151B ILE* 3.7 28.5 - - + -
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Residues in contact with ASN 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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142B ASN* 2.8 36.6 + - - +
143B ASP* 4.8 2.9 + - - +
145B PHE* 1.3 75.1 - - - +
147B SER* 1.3 61.1 + - - +
148B CYS 3.2 0.2 - - - -
149B GLY 3.0 20.5 + - - +
150B ILE* 3.5 6.8 - - - +
151B ILE* 3.2 35.1 + - - +
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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