Contacts of the strand formed by residues 177 - 182 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A LEU 3.3 0.9 - - - +
143A ILE* 3.2 26.9 - - - +
144A THR* 2.7 29.3 + - - +
145A GLU 4.5 4.4 + - - -
146A GLY* 2.9 29.7 + - - -
147A SER* 4.7 2.4 - - - +
153A PRO* 3.6 27.3 - - + +
154A SER 3.6 6.2 - - - +
155A LYS* 4.2 12.1 - - - +
176A PHE* 1.3 77.6 - - - +
178A TYR* 1.3 61.7 + - - +
179A PHE* 3.9 10.0 - - + -
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Residues in contact with TYR 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A PRO* 3.3 30.7 - - + +
71A ILE* 3.7 16.0 - - + +
72A LEU* 5.1 3.1 - - + -
75A LEU* 3.6 29.4 - - + -
141A VAL* 4.0 9.4 - - + -
142A LEU 3.4 0.9 - - - -
143A ILE* 3.5 24.5 - - + -
152A THR 4.5 0.9 - - - +
153A PRO 4.1 0.2 - - - -
154A SER 3.0 30.0 + - - +
156A GLY* 3.7 32.3 - - - -
157A PRO* 4.0 11.6 - - + +
176A PHE* 3.9 17.7 - + + -
177A ASN* 1.3 75.9 - - - +
179A PHE* 1.3 70.1 + - - +
189A LEU* 3.7 23.5 - - + +
324A TYR* 3.8 10.3 - + - +
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Residues in contact with PHE 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A PHE* 3.8 20.6 - + + -
140A GLY 3.8 0.3 - - - +
141A VAL* 3.2 8.2 - - - +
142A LEU* 2.8 54.3 + - + -
144A THR* 3.4 24.5 - - - -
148A VAL* 3.8 25.1 - - + -
151A LEU* 3.7 29.6 - - + -
152A THR 3.3 31.2 - - - -
153A PRO* 3.6 20.2 - - + -
177A ASN* 3.9 9.4 - - + -
178A TYR* 1.3 74.7 - - - +
180A LYS* 1.3 59.8 + - - +
186A ILE* 5.5 6.1 - - + -
189A LEU* 4.4 3.8 - - - -
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Residues in contact with LYS 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A ASN 5.3 0.8 + - - -
75A LEU* 2.8 37.7 + - + +
76A GLY* 4.6 3.2 - - - -
120A THR* 4.9 10.1 - - - -
134A PHE* 4.2 0.7 - - - -
140A GLY 3.4 9.0 - - - +
141A VAL* 4.2 11.4 - - + -
179A PHE* 1.3 75.4 - - - +
181A LYS* 1.3 72.4 + - - +
182A VAL* 3.9 19.9 - - + +
186A ILE* 3.7 6.8 - - - +
187A GLN* 3.0 49.5 + - + +
189A LEU* 3.9 30.5 - - + +
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Residues in contact with LYS 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A THR* 5.0 1.7 + - - +
134A PHE* 3.4 39.5 + - + +
135A ARG* 3.0 28.2 + - - +
136A ASN 4.5 0.2 - - - -
137A ALA 2.8 25.9 + - - +
138A ARG 3.8 8.7 - - - +
139A ASN* 3.3 6.4 - - - +
140A GLY 2.9 32.9 + - - +
180A LYS* 1.3 74.8 - - - +
182A VAL* 1.3 66.6 + - - +
184A GLY* 3.7 26.2 + - - -
185A ILE 3.5 7.4 - - - +
186A ILE* 3.7 23.3 - - + +
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Residues in contact with VAL 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A ASN* 3.3 7.6 - - - +
180A LYS* 3.9 15.9 - - - +
181A LYS* 1.3 78.5 - - - +
183A ASP* 1.3 83.7 + - + +
184A GLY 3.1 1.8 - - - -
185A ILE* 2.8 28.9 + - - +
187A GLN* 3.5 35.9 - - + +
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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