Contacts of the strand formed by residues 20 - 27 (chain B) in PDB entry 3C5C
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 20 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A TYR* 4.2 17.1 - - - +
143A GLN* 5.6 3.3 + - - -
19B LEU* 1.3 82.0 + - - +
21B VAL* 1.3 66.6 + - - +
22B ASN* 3.2 22.6 + - - +
69B HIS* 3.2 13.2 - - + +
71B ARG* 3.0 35.4 + - - +
92B HIS* 3.7 14.5 - - + -
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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
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19B LEU 4.6 0.7 - - - +
20B GLU* 1.3 80.3 - - - +
22B ASN* 1.3 61.7 + - - +
23B LEU* 3.6 26.2 - - + -
68B VAL* 3.5 26.7 - - + -
69B HIS 2.8 8.7 + - - +
70B LEU* 3.6 9.1 - - + +
71B ARG* 2.8 31.9 + - - +
92B HIS* 3.6 7.6 - - + +
180B VAL* 4.4 8.1 - - + -
183B ALA* 4.0 21.1 - - + -
184B ARG* 3.8 27.8 - - + +
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Residues in contact with ASN 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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138A MET* 5.6 1.2 - - - -
20B GLU* 3.2 24.2 + - - +
21B VAL* 1.3 74.2 - - - +
23B LEU* 1.3 62.7 + - - +
71B ARG* 3.5 10.3 - - - -
90B TRP* 3.0 68.9 + - + +
91B ALA* 3.6 1.3 - - - -
92B HIS* 2.7 52.7 + - - +
93B ALA 3.3 5.7 + - - -
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Residues in contact with LEU 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* 3.6 24.5 - - + -
22B ASN* 1.3 75.8 - - - +
24B ALA* 1.3 59.4 - - - +
25B ILE* 4.1 8.0 + - + -
70B LEU* 3.7 22.7 - - + -
71B ARG 2.7 13.4 + - - +
72B VAL* 3.3 6.4 - - + +
73B MET 2.8 25.6 + - - +
90B TRP* 3.6 3.6 - - - -
93B ALA* 3.4 16.8 - - + +
95B LEU* 5.1 5.2 - - + -
176B PHE* 3.7 46.4 - - + +
179B ALA* 3.9 28.3 - - + -
180B VAL 4.3 0.7 - - - +
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Residues in contact with ALA 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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23B LEU* 1.3 73.9 - - - +
25B ILE* 1.3 62.2 + - - +
26B LEU* 3.9 6.6 + - + -
73B MET* 3.6 9.4 - - + +
75B THR* 5.2 0.2 - - + -
87B TYR* 3.9 17.5 - - + -
90B TRP* 4.2 5.8 - - + -
91B ALA* 3.9 9.5 - - + +
93B ALA 3.0 7.7 + - - -
94B PHE* 3.4 32.3 - - + -
95B LEU 3.0 25.3 + - - +
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Residues in contact with ILE 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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23B LEU* 4.8 5.8 - - + -
24B ALA* 1.3 76.3 - - - +
26B LEU* 1.3 56.1 + - - +
33B LYS* 3.7 25.4 - - + +
36B LEU* 5.8 1.8 - - + -
37B THR* 4.0 9.6 - - - +
72B VAL* 3.8 29.8 - - + -
73B MET 2.8 14.1 + - - +
74B ASP* 4.4 5.4 - - - +
75B THR* 2.6 35.7 + - - +
95B LEU* 3.2 43.3 - - + +
97B VAL* 3.6 28.3 - - + -
176B PHE* 4.2 5.8 - - + -
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Residues in contact with LEU 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 ALA* 4.4 4.9 - - + +
25B ILE* 1.3 81.7 - - - +
27B GLY* 1.3 60.0 + - - +
33B LYS* 3.4 11.8 - - - +
75B THR* 3.7 20.0 - - + +
77B ASP* 5.9 0.2 - - - +
87B TYR* 3.6 46.9 - - + +
94B PHE* 3.8 22.0 - - + -
95B LEU 2.8 12.3 + - - +
96B VAL* 3.5 7.1 - - + -
97B VAL* 2.8 26.9 + - - +
112B TYR* 3.8 27.8 - - + -
115B LEU* 4.9 0.4 - - + -
116B LEU* 4.2 17.9 - - + -
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Residues in contact with GLY 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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26B LEU* 1.3 78.0 - - - +
28B ARG* 1.3 68.1 + - - -
29B ARG 3.7 0.5 + - - -
33B LYS* 3.1 17.6 + - - +
75B THR* 4.6 1.5 + - - -
77B ASP* 5.0 3.6 - - - +
96B VAL* 5.0 1.3 - - - -
97B VAL 3.5 15.5 - - - -
109B SER* 5.6 1.1 - - - -
112B TYR* 3.5 33.3 + - - -
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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