Contacts of the strand formed by residues 177 - 182 (chain E) in PDB entry 2RHB
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 177 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142E LEU 3.2 1.4 - - - +
143E ILE* 3.2 27.0 - - - +
144E THR* 2.9 25.0 + - - +
145E GLU 4.3 5.0 + - - +
146E GLY 2.7 30.0 + - - -
147E SER* 4.1 6.3 - - - +
153E PRO* 3.9 24.5 - - + +
154E SER 3.5 6.1 - - - +
155E LYS* 4.5 7.6 - - - +
175E GLN* 4.3 1.2 + - - +
176E PHE* 1.3 73.9 - - - +
178E TYR* 1.3 60.9 + - - +
179E PHE* 3.5 12.7 - - + -
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Residues in contact with TYR 178 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67E PRO* 3.1 33.8 - - + +
71E ILE* 3.4 17.5 - - + +
72E LEU* 5.4 3.4 - - + -
75E LEU* 3.5 31.4 - - + -
141E VAL* 4.0 10.3 - - + -
142E LEU 3.5 2.0 - - - -
143E ILE* 3.6 20.2 - - + -
152E THR 4.6 1.0 - - - +
153E PRO 4.0 1.4 - - - -
154E SER* 2.9 29.3 + - - +
156E GLY* 4.0 19.3 - - - -
157E PRO* 4.2 10.0 - - + +
176E PHE* 3.6 32.5 - + + -
177E ASN* 1.3 72.5 - - - +
179E PHE* 1.3 66.2 + - - +
189E LEU* 3.3 26.6 - - + +
324E TYR* 4.0 9.4 - + + +
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Residues in contact with PHE 179 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134E PHE* 3.7 20.4 - - + -
141E VAL* 3.3 6.5 - - - +
142E LEU* 2.8 48.7 + - + +
144E THR* 3.4 24.9 - - + -
148E VAL* 4.0 21.5 - - + -
151E LEU* 4.0 30.3 - - + -
152E THR 3.6 15.9 - - - +
153E PRO* 3.5 27.4 - - + -
177E ASN* 3.5 29.2 - - + -
178E TYR* 1.3 73.9 - - - +
180E LYS* 1.3 61.6 + - - +
186E ILE* 5.6 6.1 - - + -
187E GLN 5.6 1.3 - - - -
189E LEU* 4.5 2.7 - - - -
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Residues in contact with LYS 180 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74E ASN 5.4 0.6 + - - -
75E LEU* 3.2 38.6 + - + +
120E THR* 5.1 6.5 - - - -
134E PHE* 4.0 2.7 - - - -
140E GLY 3.4 12.3 - - - +
141E VAL* 3.9 12.1 - - + -
179E PHE* 1.3 76.6 - - - +
181E LYS* 1.3 70.1 + - - +
182E VAL* 3.7 24.3 - - + +
186E ILE* 3.7 6.1 - - - +
187E GLN* 2.8 36.6 + - + +
189E LEU* 3.7 30.2 - - + +
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Residues in contact with LYS 181 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120E THR* 5.3 1.2 + - - +
134E PHE* 3.4 32.0 - - + +
135E ARG* 2.5 35.6 + - - +
136E ASN 4.4 0.4 - - - -
137E ALA* 2.8 26.9 + - + +
138E ARG 3.6 12.6 - - - +
139E ASN* 3.7 4.5 - - - +
140E GLY 3.1 28.7 + - - +
180E LYS* 1.3 79.0 - - - +
182E VAL* 1.3 67.9 + - - +
184E GLY* 3.8 15.0 + - - +
185E ILE 3.4 11.9 - - - +
186E ILE* 3.8 26.7 - - + -
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Residues in contact with VAL 182 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139E ASN* 3.5 5.8 - - - +
180E LYS* 3.7 25.1 - - - +
181E LYS* 1.3 77.8 - - - +
183E ASP* 1.3 87.8 + - - +
184E GLY 3.3 0.4 - - - -
185E ILE* 3.0 26.4 + - - +
187E GLN* 3.6 24.1 + - + +
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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