Contacts of the strand formed by residues 19 - 27 (chain B) in PDB entry 6X34
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 GLU 19 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18B ASP* 1.3 72.8 - - - +
20B VAL* 1.3 63.3 + - - +
66B CYS* 5.4 4.9 - - + -
67B PHE 3.3 9.2 - - - +
68B VAL* 4.2 11.9 - - + +
204B PRO* 3.8 2.1 - - - +
205B ILE* 3.0 47.3 + - + +
206B CYS* 3.0 21.0 + - + +
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Residues in contact with VAL 20 (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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14B LEU* 5.1 12.3 - - + -
18B ASP* 3.9 12.6 - - + +
19B GLU* 1.3 78.4 - - - +
21B VAL* 1.3 68.4 + - - +
66B CYS* 4.4 0.2 - - - -
67B PHE* 2.5 58.3 + - + +
68B VAL* 4.7 4.7 - - - +
69B LEU* 4.7 12.8 - - + +
109B LEU* 6.1 1.1 - - + -
202B MET* 3.6 22.4 - - + -
204B PRO* 4.3 17.3 - - + -
205B ILE* 4.5 0.4 - - - +
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Residues in contact with VAL 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B VAL* 1.3 81.2 - - - +
22B LEU* 1.3 63.8 + - - +
23B GLN* 4.0 4.5 + - + +
36B CYS* 3.7 27.1 - - - -
62B LEU* 5.5 3.1 - - + +
65B CYS* 3.7 28.9 - - - +
66B CYS* 4.7 1.8 - - - -
67B PHE* 4.9 1.6 - - + -
201B ASN 4.3 0.3 - - - +
202B MET* 3.2 13.4 - - - +
203B ASN* 3.4 18.7 + - - +
205B ILE* 3.8 34.1 - - + +
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Residues in contact with LEU 22 (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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21B VAL* 1.3 73.7 - - - +
23B GLN* 1.3 62.7 + - - +
24B CYS* 6.2 0.4 - - + -
36B CYS* 3.2 24.8 - - - -
37B LEU* 4.2 21.3 + - + +
67B PHE* 4.6 20.1 - - + -
109B LEU* 5.9 7.2 - - + -
171B LEU* 5.7 9.9 - - + -
200B TRP* 3.9 24.9 - - + -
201B ASN 3.3 20.4 - - - +
202B MET* 3.6 23.2 - - + +
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Residues in contact with GLN 23 (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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21B VAL* 5.0 4.3 - - + +
22B LEU* 1.3 79.4 - - - +
24B CYS* 1.3 64.1 + - - +
34B LYS* 3.4 24.7 - - + +
35B LEU 3.4 16.2 - - - +
36B CYS* 5.0 4.5 - - + +
37B LEU 5.7 0.2 - - - +
52B THR* 3.5 25.3 - - + +
53B SER* 5.2 0.6 + - - +
200B TRP* 3.8 1.6 - - - +
201B ASN* 2.7 53.2 + - + +
203B ASN* 6.1 1.2 - - - +
268B SER* 4.9 8.7 + - - -
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Residues in contact with CYS 24 (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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22B LEU* 6.2 0.7 - - + -
23B GLN* 1.3 76.5 - - - +
25B ASN* 1.3 61.1 + - - +
34B LYS* 3.3 7.0 - - - +
35B LEU* 3.2 31.0 + - + +
49B LEU* 6.2 0.2 - - + -
182B LEU* 4.0 35.8 - - + +
198B THR* 5.8 0.4 - - + -
199B LEU* 4.5 13.2 - - - +
200B TRP* 4.9 6.7 - - + +
201B ASN* 4.8 2.9 - - - +
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Residues in contact with ASN 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 CYS* 1.3 77.1 - - - +
26B ALA* 1.3 85.5 + - - +
27B THR* 4.0 2.2 + - - -
32B GLN* 4.4 16.1 - - - +
33B LEU 3.2 18.4 + - - +
34B LYS* 4.2 7.9 - - + +
182B LEU* 5.1 3.6 - - - +
198B THR* 5.6 6.1 - - - +
199B LEU* 5.3 12.6 + - + +
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Residues in contact with ALA 26 (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 CYS 4.2 0.8 + - - +
25B ASN* 1.3 79.3 + - - +
27B THR* 1.3 61.1 + - - +
28B VAL* 3.0 10.0 + - + +
33B LEU* 2.8 35.9 + - + +
35B LEU* 5.9 4.7 - - + +
49B LEU* 6.4 0.7 - - + -
182B LEU* 4.9 15.0 - - + -
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Residues in contact with THR 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 ASN* 4.0 4.5 + - - -
26B ALA* 1.3 68.0 - - - +
28B VAL* 1.3 65.9 + - - +
31B GLU 4.9 1.8 - - - -
32B GLN* 5.1 4.3 - - - +
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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