Contacts of the strand formed by residues 19 - 25 (chain B) in PDB entry 5EBW
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 VAL 19 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B LEU* 3.9 27.8 - - + -
13B VAL* 4.4 13.2 - - + -
17B GLU 3.9 0.8 + - - -
18B ARG* 1.3 73.6 - - - +
20B SER* 1.3 67.9 + - - +
21B PHE* 3.7 25.1 - - + -
74B SER* 3.3 5.4 - - - -
75B ILE* 3.0 42.8 + - + +
78B VAL* 3.6 25.4 - - + -
104B LEU* 4.1 15.5 - - + -
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Residues in contact with SER 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PRO* 6.0 0.3 - - - +
11B LEU* 3.4 18.5 - - - +
18B ARG* 4.8 7.3 + - - +
19B VAL* 1.3 77.6 + - - +
21B PHE* 1.3 61.9 + - - +
22B SER* 3.9 2.6 + - - -
72B THR* 3.8 17.4 - - - +
73B LEU 3.3 4.0 - - - -
74B SER* 3.0 16.3 + - - -
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Residues in contact with PHE 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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6B GLN* 5.5 0.2 - - - +
11B LEU* 3.6 15.5 - - + -
19B VAL* 3.7 19.1 - - + -
20B SER* 1.3 73.2 - - - +
22B SER* 1.3 60.7 + - - +
35B TRP* 3.9 19.8 - - + -
72B THR* 3.3 10.2 - - - +
73B LEU* 2.7 55.4 + - + +
75B ILE* 3.7 23.8 - - + -
86B TYR* 3.5 42.2 - + + -
102B THR* 3.5 33.9 - - + -
104B LEU* 4.0 20.4 - - + -
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Residues in contact with SER 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B THR 4.4 1.7 + - - -
6B GLN* 3.3 28.4 + - - +
7B SER 3.5 23.7 + - - -
8B PRO* 6.0 0.8 - - - +
20B SER 3.9 2.6 + - - -
21B PHE* 1.3 76.4 - - - +
23B CYS* 1.3 66.6 + - - +
24B ARG* 4.8 4.2 + - - +
35B TRP* 4.3 1.9 - - - -
71B PHE 3.7 4.5 + - - -
72B THR* 4.9 1.8 - - - +
102B THR* 4.8 2.9 + - - -
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Residues in contact with CYS 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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4B LEU* 4.3 10.1 - - - -
5B THR 3.6 3.8 - - - -
6B GLN* 4.5 1.1 - - - -
22B SER* 1.3 76.7 + - - +
24B ARG* 1.3 61.5 + - - +
33B ILE* 4.1 16.2 - - - -
35B TRP* 3.6 22.7 - - + -
69B THR 3.6 1.6 - - - +
70B ASP* 3.8 0.5 - - - -
71B PHE* 2.8 45.2 + - + +
88B CYS* 2.0 50.5 - - - -
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Residues in contact with ARG 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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3B LEU 3.5 1.0 - - - +
4B LEU* 3.4 4.8 - - - -
5B THR* 2.7 50.3 + - - +
22B SER* 4.3 5.4 - - - +
23B CYS* 1.3 75.0 - - - +
25B ALA* 1.3 72.0 + - - +
69B THR* 3.2 5.4 - - - +
70B ASP* 3.0 33.2 + - - +
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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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2B ILE* 4.2 4.7 - - + -
3B LEU 3.3 5.2 - - - +
4B LEU* 3.6 12.1 - - + +
23B CYS 4.3 0.2 - - - -
24B ARG* 1.3 81.0 - - - +
26B SER* 1.3 59.9 + - - +
27B GLN 3.1 24.5 + - - +
29B ILE* 3.6 27.8 - - + -
69B THR* 2.9 27.6 + - - +
71B PHE* 4.8 1.3 - - + -
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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