Contacts of the strand formed by residues 170 - 176 (chain X) in PDB entry 3RCI
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 VAL 170 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71X VAL* 3.9 5.7 - - - +
129X ASN* 5.1 1.3 + - - +
130X PHE* 5.9 0.6 - - - +
132X LEU* 3.5 53.6 + - + +
133X LYS 3.9 9.6 - - - +
134X HIS* 3.4 43.7 - - + +
139X VAL* 3.5 16.4 - - + -
140X LEU 3.5 13.2 - - - +
141X SER* 3.9 2.0 - - - +
168X HIS 3.4 1.0 + - - +
169X VAL* 1.3 80.5 - - - +
171X PHE* 1.3 63.8 + - - +
172X GLY 4.1 9.4 - - - +
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Residues in contact with PHE 171 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66X LEU* 3.5 9.6 - - + +
67X LYS* 2.7 34.1 + - - -
71X VAL* 3.5 21.1 - - + -
74X THR* 3.7 19.5 - - + -
75X ALA* 4.6 5.1 - - - +
78X PHE* 3.5 42.0 - + + -
132X LEU* 4.4 1.6 - - - -
140X LEU* 3.0 40.8 + - + -
141X SER* 3.5 19.3 - - - -
142X MET* 3.4 30.7 - - + -
154X PHE* 4.3 1.8 - - + -
169X VAL 3.6 13.0 - - - -
170X VAL* 1.3 75.5 - - - +
172X GLY* 1.3 54.2 + - - +
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Residues in contact with GLY 172 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65X GLU 3.0 15.0 - - - -
67X LYS* 4.1 11.6 - - - +
132X LEU* 4.9 0.6 - - - +
139X VAL* 3.9 2.8 - - - +
140X LEU* 2.9 32.0 + - - +
170X VAL* 3.9 8.8 - - - +
171X PHE* 1.3 80.1 - - - +
173X HIS* 1.3 66.7 + - - +
210X M3I 5.2 0.7 - - - +
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Residues in contact with HIS 173 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64X LEU* 3.4 8.0 - - - -
65X GLU* 3.0 59.5 + - + +
67X LYS* 4.3 17.0 - - - +
138X GLY 3.1 15.0 - - - +
139X VAL* 4.4 0.2 - - - -
140X LEU* 4.0 4.2 - - - +
172X GLY* 1.3 77.0 - - - +
174X VAL* 1.3 85.9 + - - +
175X ILE* 3.6 14.7 - - - +
210X M3I 3.6 34.2 - + + +
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Residues in contact with VAL 174 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62X VAL* 4.1 9.4 - - + -
63X VAL 3.5 4.9 - - - +
64X LEU* 3.7 14.8 - - + -
138X GLY* 2.8 25.0 + - - +
156X ILE* 3.7 24.5 - - + -
173X HIS* 1.3 83.8 - - - +
175X ILE* 1.3 57.9 + - - +
176X GLU* 3.3 32.8 - - - +
177X GLY 4.2 1.6 - - - -
178X MET* 3.9 33.8 - - + +
181X VAL* 4.3 1.1 - - + -
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Residues in contact with ILE 175 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47X LEU* 4.0 16.6 - - + -
63X VAL* 2.8 24.2 + - + +
65X GLU* 3.7 41.1 - - + +
173X HIS* 3.6 21.5 - - - +
174X VAL* 1.3 73.2 - - - +
176X GLU* 1.3 65.1 + - + +
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Residues in contact with GLU 176 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61X ARG* 4.6 14.0 - - - +
62X VAL* 3.5 0.9 - - - -
63X VAL* 2.9 49.2 + - + +
174X VAL* 3.3 12.6 - - - +
175X ILE* 1.3 83.0 - - + +
177X GLY* 1.3 65.3 + - - +
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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