Contacts of the strand formed by residues 23 - 27 (chain B) in PDB entry 1RXV
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 LYS 23 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B GLY 4.2 2.4 + - - +
22B LYS* 1.3 72.4 - - - +
24B ILE* 1.3 60.8 - - - +
74B ARG* 3.2 20.2 - - + +
76B VAL* 5.2 1.1 - - + -
163B GLY 5.6 0.4 + - - -
164B ASP* 3.4 20.8 + - - +
165B VAL* 3.4 18.9 - - + +
166B GLU* 3.0 27.3 + - - +
167B TYR 3.5 4.5 + - - -
290B ILE* 4.0 31.4 - - + -
292B PHE* 4.5 5.8 - - + -
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Residues in contact with ILE 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B PHE* 4.0 21.3 - - + -
22B LYS* 4.0 8.7 - - + +
23B LYS* 1.3 79.4 - - - +
25B ALA* 1.3 56.1 + - - +
26B VAL* 3.2 20.0 + - + -
68B MET* 5.9 1.3 - - - -
73B ILE* 3.6 23.8 - - + -
74B ARG 3.0 8.5 + - - +
75B PRO* 3.4 4.6 - - + +
76B VAL* 2.7 32.6 + - - -
165B VAL* 4.4 3.4 - - - -
167B TYR* 3.3 21.1 - - + +
168B THR 4.1 1.8 - - - -
169B GLY* 3.8 21.3 - - - +
184B ALA* 5.2 0.9 - - + -
187B LEU* 3.6 28.0 - - + -
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Residues in contact with ALA 25 (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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24B ILE* 1.3 66.7 - - - +
26B VAL* 1.3 63.3 + - - +
27B ASP 3.6 1.0 + - - -
76B VAL* 3.3 10.1 - - - -
78B VAL* 4.1 8.1 - - + -
156B ALA* 3.6 33.0 - - + +
159B MET* 4.5 7.0 - - + -
165B VAL* 3.7 28.2 - - + +
167B TYR 2.8 11.5 + - - +
168B THR* 3.5 4.4 - - + -
169B GLY 3.2 17.3 + - - -
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Residues in contact with VAL 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ILE* 3.8 24.5 - - + +
25B ALA* 1.3 70.3 - - - +
27B ASP* 1.3 59.4 + - - +
28B ALA 3.0 3.1 + - - -
31B THR* 3.0 32.1 - - + +
68B MET* 5.5 7.4 - - + -
75B PRO* 4.1 18.8 - - + -
76B VAL 2.7 11.9 + - - +
77B PHE* 3.4 21.1 - - + -
78B VAL* 2.9 29.2 + - - -
169B GLY* 3.7 12.8 - - - +
187B LEU* 6.1 4.0 - - + +
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Residues in contact with ASP 27 (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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25B ALA 3.6 3.0 + - - -
26B VAL* 1.3 68.0 - - - +
28B ALA* 1.3 63.2 + - - +
29B PHE* 3.6 10.2 + - - +
30B ASN* 2.9 31.1 + - + +
31B THR* 2.9 24.4 + - - -
78B VAL* 4.1 7.2 - - - -
80B ASP* 4.6 2.6 - - - +
152B GLY* 3.5 6.1 - - - -
153B GLU* 3.0 64.8 + - - +
156B ALA* 5.4 2.9 - - + -
169B GLY 3.0 17.6 + - - +
170B SER* 4.2 2.9 - - - -
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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