Contacts of the strand formed by residues 144 - 154 (chain B) in PDB entry 3RBH
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 144 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B TYR 4.8 1.0 - - - +
136B ALA* 3.7 15.6 - - - +
138B LEU* 3.6 18.1 + - - +
139B THR* 2.9 47.7 + - + +
141B TYR* 3.1 17.5 + - + +
142B PRO 3.1 4.0 - - - +
143B GLY* 1.3 78.6 - - - +
145B HIS* 1.3 76.9 + - - +
146B LEU 4.5 0.2 + - - -
170B TRP* 2.9 29.8 + - + +
171B SER 3.3 11.0 - - - +
172B PHE* 3.8 22.4 - - + -
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Residues in contact with HIS 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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134B ASP* 2.9 33.3 + - - +
135B TYR 3.5 8.1 - - - +
136B ALA* 4.1 6.3 - - + -
142B PRO 5.5 1.6 - - - -
143B GLY 4.1 10.3 + - - -
144B GLU* 1.3 88.1 - - - +
146B LEU* 1.3 61.6 - - - +
147B ARG* 3.7 29.5 + - + +
169B ASN 4.0 1.1 - - - +
170B TRP* 3.7 1.7 - - - -
171B SER* 2.9 58.5 + - - +
173B GLU* 5.5 2.4 + - - -
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Residues in contact with LEU 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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133B VAL 4.0 0.7 - - - +
134B ASP* 3.3 4.6 - - - +
135B TYR* 2.9 45.2 + - + +
138B LEU* 4.7 18.4 - - + -
144B GLU* 4.5 0.4 + - - +
145B HIS* 1.3 74.0 - - - +
147B ARG* 1.3 60.4 + - - +
148B PHE* 5.8 0.9 - - + -
168B LEU* 3.5 37.7 - - + -
169B ASN 3.4 21.5 - - - +
170B TRP* 3.8 21.5 - - + +
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Residues in contact with ARG 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B SER* 5.4 0.4 + - - -
130B GLU* 5.5 1.2 + - - -
132B TRP* 3.5 64.4 - - + +
133B VAL 3.7 1.8 - - - -
134B ASP* 2.9 27.9 + - - +
145B HIS* 3.7 23.9 + - + +
146B LEU* 1.3 73.5 - - - +
148B PHE* 1.3 64.2 + - - +
151B GLN* 3.2 35.2 + - - +
152B ARG 5.7 3.6 + - - +
168B LEU* 3.3 4.5 - - - +
169B ASN* 2.8 36.5 + - + +
446B SER 5.3 9.3 + - - -
448B SER* 5.8 5.5 - - - -
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Residues in contact with PHE 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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132B TRP* 3.0 5.1 - - - +
133B VAL* 2.9 52.8 + - + +
146B LEU* 5.8 0.7 - - + -
147B ARG* 1.3 78.1 - - - +
149B GLY* 1.3 67.7 + - - +
151B GLN* 4.1 0.2 - - - -
167B ALA 3.4 6.5 - - - -
168B LEU* 3.9 26.9 - - + -
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Residues in contact with GLY 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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131B PHE* 3.5 10.8 - - - -
132B TRP* 4.3 1.1 - - - -
148B PHE* 1.3 87.6 - - - +
150B ARG* 1.3 60.3 + - - -
151B GLN* 3.0 13.7 + - - -
166B GLU* 4.0 3.4 - - - -
167B ALA 2.8 31.2 + - - -
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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
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128B ALA 3.4 8.7 + - - -
129B ARG* 2.6 44.0 + - - +
130B GLU* 3.6 3.8 - - - -
131B PHE* 2.9 70.7 + - + +
132B TRP* 3.1 9.4 - - - -
149B GLY* 1.3 69.9 - - - -
151B GLN* 1.3 59.2 + - - +
164B ASN* 3.2 31.3 + - - +
165B ILE* 3.3 20.9 - - - +
166B GLU* 3.8 12.2 + - + +
186B ARG* 3.7 10.7 - - - +
188B SER 4.7 4.4 + - - -
189B GLU* 4.3 18.6 + - - -
190B TYR* 3.7 23.0 - - - -
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Residues in contact with GLN 151 (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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130B GLU* 3.7 7.0 - - - -
132B TRP* 3.6 15.5 - - + +
147B ARG* 3.2 46.6 + - - +
148B PHE 3.9 0.6 - - - +
149B GLY 3.0 11.1 + - - +
150B ARG* 1.3 77.3 - - - +
152B ARG* 1.3 66.4 + - - +
153B LEU* 3.3 12.0 + - + +
164B ASN* 3.3 7.1 - - - -
165B ILE* 2.9 35.8 + - - +
167B ALA* 2.9 41.1 + - + -
169B ASN* 3.4 18.6 + - - +
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Residues in contact with ARG 152 (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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102B ASP* 5.7 2.9 + - - -
130B GLU* 3.4 7.9 + - - +
147B ARG* 5.7 3.6 + - - +
151B GLN* 1.3 77.3 - - - +
153B LEU* 1.3 60.7 + - - +
154B ARG* 3.6 30.3 + - + +
162B ASP* 2.8 31.0 + - - -
163B THR* 3.4 18.1 - - - +
164B ASN* 3.4 15.8 + - - +
169B ASN* 5.7 0.7 + - - -
362B ARG* 3.6 18.6 - - - +
448B SER* 3.5 51.8 + - - +
449B GLN* 4.7 4.9 - - - +
451B VAL* 5.2 2.6 - - - +
452B ASP* 3.7 11.3 + - - -
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Residues in contact with LEU 153 (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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151B GLN* 3.3 8.5 + - + +
152B ARG* 1.3 71.0 - - - +
154B ARG* 1.3 59.4 + - - +
161B GLN* 3.3 23.1 - - + +
162B ASP* 3.1 8.0 + - - -
163B THR* 2.8 35.0 + - + +
165B ILE* 3.4 31.4 - - + -
167B ALA* 4.2 10.5 - - + -
169B ASN* 3.8 39.5 - - + +
184B ALA* 4.0 6.1 - - + -
208B PHE* 3.5 28.7 - - + -
349B LEU* 4.7 9.0 - - + -
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Residues in contact with ARG 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B ARG* 3.6 25.9 + - + +
153B LEU* 1.3 75.7 - - - +
155B GLU* 1.3 71.7 + - - +
156B ASP* 4.1 32.4 + - - +
161B GLN* 3.3 11.9 + - - +
162B ASP* 3.3 29.2 - - - +
353B ARG 5.6 0.2 + - - -
354B SER* 6.0 0.6 - - - +
355B ASN* 4.8 6.9 + - - -
362B ARG* 3.5 27.3 - - - +
448B SER 5.5 1.8 + - - -
451B VAL* 3.9 24.3 - - - +
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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