Contacts of the strand formed by residues 30 - 35 (chain B) in PDB entry 6YB9
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 30 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B GLU* 4.7 0.5 - - - +
24B LEU* 3.9 15.0 + - + +
27B SER* 3.4 34.5 + - - +
28B PRO* 3.2 8.6 + - + +
29B GLY* 1.3 81.8 + - - +
31B VAL* 1.3 70.3 + - - +
78B THR* 3.6 35.0 - - + +
87B ILE* 4.3 13.7 - - + -
88B ALA 3.3 12.1 - - - +
89B PRO* 4.4 9.2 - - + +
90B GLN* 4.1 1.3 + - - +
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Residues in contact with VAL 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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13B LEU* 4.3 15.3 - - + -
21B VAL* 3.9 15.0 - - + -
22B TYR 3.3 16.4 - - - +
23B GLU* 4.4 2.9 - - + -
24B LEU* 3.9 7.9 - - - -
30B LYS* 1.3 78.8 - - - +
32B LEU* 1.3 58.4 + - - +
33B LEU* 3.8 18.7 - - + +
87B ILE* 3.4 5.0 - - - +
88B ALA 2.8 41.4 + - - +
90B GLN* 3.8 39.3 - - + +
702B ANP 4.1 8.5 - - - +
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Residues in contact with LEU 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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7B LEU* 4.6 3.6 - - + -
9B ILE* 4.1 22.9 - - + -
20B GLU 3.5 2.1 - - - +
21B VAL* 3.4 4.3 - - - -
22B TYR* 2.9 54.6 + - + +
24B LEU* 4.0 16.0 - - + +
31B VAL* 1.3 72.8 - - - +
33B LEU* 1.3 60.6 + - - +
34B GLN* 3.8 10.5 + - + +
81B CYS* 4.0 14.1 - - + -
85B ALA* 3.7 28.3 - - + -
86B PHE 3.6 6.1 - - - +
87B ILE* 3.6 23.1 - - + +
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Residues in contact with LEU 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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19B LYS* 4.0 24.4 - - + +
20B GLU 3.5 5.2 - - - -
21B VAL* 4.0 13.5 - - + -
31B VAL* 3.8 21.3 - - + +
32B LEU* 1.3 70.3 - - - +
34B GLN* 1.3 59.5 + - - +
35B SER* 3.9 2.1 + - - -
58B ASN* 4.5 0.5 - - - +
85B ALA* 3.2 6.4 - - - -
86B PHE* 3.0 60.4 + - + +
88B ALA* 3.7 29.6 - - + -
207B ASP 5.1 0.9 - - - +
702B ANP 3.4 39.7 - - + +
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Residues in contact with GLN 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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19B LYS* 3.2 4.3 - - - -
20B GLU* 2.7 57.8 + - + +
22B TYR* 4.1 18.6 - - + +
32B LEU* 3.8 9.7 + - + +
33B LEU* 1.3 71.5 - - - +
35B SER* 1.3 73.0 + - - +
36B LYS* 4.5 1.5 - - + +
84B THR* 2.7 37.0 + - - +
85B ALA* 3.8 16.1 - - + +
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Residues in contact with SER 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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18B THR 3.5 8.2 + - - -
19B LYS* 4.2 13.2 - - - +
33B LEU 3.9 1.6 + - - -
34B GLN* 1.3 91.5 - - - +
36B LYS* 1.3 60.8 + - - +
54B ALA* 3.5 33.6 + - - +
57B SER* 4.4 12.8 - - - -
58B ASN* 4.4 9.7 + - - +
84B THR* 2.9 17.8 + - - -
86B PHE* 5.9 1.7 - - - -
208B VAL* 5.8 2.1 - - - +
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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