Contacts of the strand formed by residues 29 - 36 (chain B) in PDB entry 3RPF
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 ALA 29 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B ALA* 5.5 0.2 - - - +
27B PHE* 3.7 3.0 - - - +
28B GLY* 1.3 80.5 - - - +
30B PHE* 1.3 62.1 + - - +
31B CYS* 4.2 4.0 - - - -
93B SER 4.7 0.2 - - - -
94B MSE 3.3 7.5 - - - +
95B GLY 3.1 25.5 + - - +
97B ASN 3.8 5.2 - - - +
98B ARG* 3.5 41.7 - - + +
101B ALA* 4.6 7.2 - - + -
146B SO4 4.4 1.6 - - - +
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Residues in contact with PHE 30 (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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15B LEU* 4.1 10.3 - - + -
18B TYR* 3.6 31.6 - - + -
19B GLN* 3.7 40.4 - - + -
22B ALA* 3.9 21.5 - - + -
28B GLY 5.7 0.9 - - - +
29B ALA* 1.3 75.8 - - - +
31B CYS* 1.3 59.7 + - - +
32B VAL* 3.4 26.2 + - + +
92B VAL* 3.6 21.3 - - + -
93B SER 4.0 2.0 - - - -
94B MSE 4.1 4.3 - - - -
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Residues in contact with CYS 31 (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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29B ALA* 5.1 3.6 - - - -
30B PHE* 1.3 77.9 - - - +
32B VAL* 1.3 62.3 + - - +
91B CYS 3.9 0.2 - - - +
92B VAL* 3.2 8.0 - - - +
93B SER* 2.8 45.0 + - - +
101B ALA* 4.2 15.3 - - - -
102B LEU* 3.6 37.9 - - + -
105B TYR* 3.5 25.5 - - + -
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Residues in contact with VAL 32 (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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15B LEU* 3.6 31.4 - - + -
30B PHE* 3.4 38.0 + - + -
31B CYS* 1.3 79.4 - - - +
33B PHE* 1.3 64.5 + - - +
34B VAL* 4.0 19.7 - - + -
90B LEU* 4.5 1.1 - - + -
91B CYS 3.4 5.2 - - - +
92B VAL* 4.3 7.4 - - + -
105B TYR* 2.8 17.2 + - - -
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Residues in contact with PHE 33 (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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32B VAL* 1.3 75.0 - - - +
34B VAL* 1.3 74.5 + - - +
35B GLY* 3.7 19.3 - - - -
89B PHE* 3.7 29.4 - + - -
90B LEU* 3.2 5.2 - - - +
91B CYS* 2.9 38.1 + - - +
105B TYR* 3.5 17.2 - - + +
109B ILE* 3.7 34.8 - - + -
113B LYS* 5.5 9.9 - - - -
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Residues in contact with VAL 34 (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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11B THR* 3.9 14.8 - - + +
15B LEU* 4.7 2.7 - - + -
32B VAL* 4.0 11.4 - - + -
33B PHE* 1.3 91.5 - - - +
35B GLY* 1.3 64.5 + - - +
36B ILE* 3.8 19.2 + - + +
87B SER* 3.5 33.7 - - - +
89B PHE 3.4 6.5 - - - +
90B LEU* 3.6 24.5 - - + -
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Residues in contact with GLY 35 (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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33B PHE* 3.7 17.1 - - - -
34B VAL* 1.3 71.3 - - - +
36B ILE* 1.3 60.2 + - - -
87B SER* 3.4 5.7 - - - -
88B SER* 3.1 31.1 + - - -
89B PHE* 2.8 23.5 + - - +
74C GLY 5.2 4.0 - - - -
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Residues in contact with ILE 36 (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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34B VAL* 3.8 25.5 + - + +
35B GLY* 1.3 76.7 - - - -
37B VAL* 1.3 74.8 + - - +
38B ARG* 3.3 10.5 + - + +
85B GLY* 4.0 18.4 - - - +
86B GLN 3.6 11.9 - - - +
87B SER* 4.2 5.4 - - - +
88B SER* 5.1 0.7 - - - -
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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