Contacts of the strand formed by residues 32 - 38 (chain E) in PDB entry 5EEY
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 PHE 32 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22E ILE* 3.6 28.3 - - + -
23E GLY 3.3 6.3 - - - +
24E LEU* 3.8 7.9 - - + +
25E THR* 4.8 1.1 - - - -
31E ARG* 1.3 84.9 - - + +
33E HIS* 1.3 61.5 + - - +
34E HIS* 3.6 20.4 - - - -
35E SER* 4.1 21.1 - - - -
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Residues in contact with HIS 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D GLY 5.2 0.4 - - - -
28D ALA* 4.6 10.9 + - - +
30D THR* 4.5 2.6 + - - -
101D TRP* 4.1 23.8 - + - -
23E GLY 2.9 25.6 + - - -
25E THR* 3.6 28.5 - - + -
32E PHE* 1.3 77.7 - - - +
34E HIS* 1.3 79.5 + - + +
51E HIS* 3.4 25.3 + - + +
52E THR* 2.6 30.8 + - - -
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Residues in contact with HIS 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D LEU* 5.3 0.4 - - + -
30D THR* 3.5 43.1 + - + +
101D TRP* 3.8 21.8 - + + -
21E VAL 3.9 0.5 - - - +
22E ILE* 3.6 2.3 - - - -
23E GLY 3.0 26.3 + - - -
32E PHE* 3.6 10.6 - - - -
33E HIS* 1.3 102.7 + - + +
35E SER* 1.3 84.9 + - - +
36E GLU* 2.8 33.5 + - + +
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Residues in contact with SER 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E ASN* 2.8 27.9 + - - -
21E VAL 3.4 6.7 - - - -
22E ILE* 4.9 2.9 - - - -
32E PHE* 4.1 17.4 - - - -
34E HIS* 1.3 87.1 + - - +
36E GLU* 1.3 58.7 + - - +
37E LYS* 4.0 11.3 + - - +
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Residues in contact with GLU 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D LEU* 3.8 21.3 - - + +
30D THR* 4.9 0.2 - - - +
32D PHE* 3.6 18.6 - - - -
56D LYS* 2.8 30.6 + - - +
101D TRP* 5.5 2.0 - - + -
19E VAL 3.8 0.5 - - - +
21E VAL* 2.8 40.3 + - + +
34E HIS* 2.8 37.7 + - + +
35E SER* 1.3 73.8 - - - +
37E LYS* 1.3 63.2 + - - +
38E LEU* 3.9 4.0 + - + +
44E LEU* 4.1 28.9 - - + -
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Residues in contact with LYS 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D LYS* 2.9 23.2 + - - -
58D ARG* 5.2 0.3 + - - -
18E GLY* 4.7 18.4 - - - +
19E VAL 3.1 9.2 - - - +
20E ASN* 4.0 25.1 - - - +
35E SER* 4.0 9.1 + - - +
36E GLU* 1.3 76.0 - - - +
38E LEU* 1.3 61.1 + - - +
39E ASP* 4.4 1.5 + - - +
42E GLU* 4.2 0.5 - - - +
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Residues in contact with LEU 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D LYS* 3.8 28.0 - - + +
12E ILE* 3.9 39.9 - - + +
14E ALA* 3.8 16.6 - - + -
16E GLU 3.8 2.3 - - - +
18E GLY* 3.1 19.2 + - - -
19E VAL* 2.8 19.6 + - + +
21E VAL* 4.0 17.3 - - + -
36E GLU* 4.4 2.5 - - + +
37E LYS* 1.3 76.0 - - - +
39E ASP* 1.3 66.0 + - - +
42E GLU* 3.3 19.1 - - + +
44E LEU* 3.9 25.1 - - + +
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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