Contacts of the strand formed by residues 19 - 25 (chain D) in PDB entry 5EEZ
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12D ILE* 4.6 0.2 - - + -
14D ALA* 3.8 8.7 - - + -
16D GLU* 3.5 20.9 - - + +
18D GLY* 1.3 76.4 - - - +
20D ASN* 1.3 64.3 + - - +
21D VAL* 4.6 0.7 - - + -
36D GLU 3.5 0.5 - - - +
37D LYS* 3.2 5.7 - - - -
38D LEU* 2.8 50.2 + - + +
57D VAL* 4.1 20.0 - - + -
58D ARG 3.5 11.7 - - - +
59D GLY 4.1 0.4 - - - -
60D LYS 3.3 36.3 - - - +
61D ALA* 4.2 9.0 - - + -
75D LYS* 4.3 1.1 - - - +
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Residues in contact with ASN 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D GLY 3.6 5.1 + - - +
19D VAL* 1.3 77.8 - - - +
21D VAL* 1.3 62.5 + - - +
22D ILE* 4.0 15.5 - - + +
35D SER* 3.3 23.7 + - - +
36D GLU 3.6 1.3 - - - -
37D LYS* 4.1 15.6 - - - +
56D LYS 3.7 1.4 - - - +
57D VAL* 3.4 7.3 - - - +
58D ARG* 2.9 42.4 + - + +
75D LYS* 3.5 20.6 - - - +
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Residues in contact with VAL 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C TRP* 4.4 12.7 - - + -
12D ILE* 3.8 36.6 - - + -
19D VAL* 4.6 1.3 - - + -
20D ASN* 1.3 76.3 - - - +
22D ILE* 1.3 61.5 + - - +
23D GLY 4.1 0.3 + - - -
34D HIS 3.8 1.4 - - - +
35D SER* 3.6 0.7 - - - -
36D GLU* 2.9 40.2 + - + +
38D LEU* 3.6 31.4 - - + -
44D LEU* 3.8 24.2 - - + -
46D ALA* 5.1 0.9 - - + -
55D ILE* 3.8 18.4 - - + -
56D LYS 3.7 2.5 - - - +
57D VAL* 4.6 3.6 - - + +
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Residues in contact with ILE 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C TRP* 4.0 2.5 - - - -
20D ASN* 4.0 18.6 - - + +
21D VAL* 1.3 77.5 - - - +
23D GLY* 1.3 61.6 + - - +
24D LEU* 3.7 2.2 - - + +
32D PHE* 3.4 50.3 - - + -
34D HIS 3.4 7.4 - - - +
35D SER* 3.7 18.6 - - - +
55D ILE* 3.3 7.6 - - - +
56D LYS* 2.9 48.9 + - + +
58D ARG* 3.6 35.7 - - + +
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Residues in contact with GLY 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C TRP* 3.5 26.7 - - - -
22D ILE* 1.3 74.2 - - - +
24D LEU* 1.3 61.1 + - - -
32D PHE* 3.4 5.9 - - - -
33D HIS* 3.0 34.8 + - - -
34D HIS 3.0 11.1 + - - -
52D THR* 3.9 5.4 - - - -
54D ALA 3.8 4.0 - - - -
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Residues in contact with LEU 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D ILE 3.7 10.5 - - - +
23D GLY* 1.3 79.3 - - - -
25D THR* 1.3 66.2 + - - +
30D THR* 3.9 21.1 - - + -
31D ARG 3.3 6.5 - - - +
32D PHE* 3.9 24.2 - - + -
33D HIS* 4.0 2.2 - - - -
52D THR* 3.4 5.4 - - - -
53D SER 3.3 19.9 + - - -
54D ALA* 2.9 40.6 + - + +
56D LYS* 4.2 14.6 - - + +
101D TRP* 5.1 3.1 - - + -
34E HIS* 4.7 1.8 - - + +
36E GLU* 3.8 33.9 - - + +
44E LEU* 4.5 4.3 - - + -
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Residues in contact with THR 25 (chain D).
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* 1.3 72.3 - - - +
26D ARG* 1.3 64.4 + - - +
29D ASP* 2.8 30.0 + - - +
30D THR* 4.2 1.0 - - - -
31D ARG* 2.8 48.9 + - + +
33D HIS* 3.7 25.1 - - + -
51D HIS 3.5 7.4 - - - +
53D SER* 4.1 0.4 - - - -
101D TRP* 2.8 27.4 + - - +
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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