Contacts of the strand formed by residues 32 - 37 (chain D) in PDB entry 5U72
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 LEU 32 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22D CYS* 4.3 2.7 - - - +
24D TYR* 3.7 31.4 - - + -
29D PHE* 3.6 8.9 - - + -
31D GLY* 1.3 74.4 - - - +
33D PHE* 1.3 68.0 + - - +
34D TRP* 3.5 24.4 - - + +
47D SER 3.9 0.3 - - - +
48D TYR* 3.3 4.7 - - - -
49D ASN* 2.7 42.0 + - + +
64D LEU* 4.6 5.2 - - + -
71D SER* 3.5 38.8 - - - +
88D CYS* 3.9 15.0 - - - -
89D ALA 3.4 4.0 - - - +
90D VAL* 3.7 13.7 - - + -
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Residues in contact with PHE 33 (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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31D GLY 4.6 1.6 - - - -
32D LEU* 1.3 80.6 - - - +
34D TRP* 1.3 63.3 + - - +
35D TYR* 3.5 34.3 - + + -
45D PHE* 3.8 22.7 - + - -
47D SER 3.3 3.6 - - - +
48D TYR* 3.3 39.0 - + + -
87D LEU 3.6 0.7 - - - +
88D CYS* 3.5 4.3 - - - -
89D ALA* 2.6 46.3 + - + +
91D LYS* 4.2 31.6 - - + -
97D LEU* 4.2 16.6 - - + -
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Residues in contact with TRP 34 (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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6D GLN* 3.6 22.9 - - - -
20D ILE* 3.4 39.9 - - + -
21D ASN 4.3 0.9 - - - -
22D CYS* 3.4 28.9 - - + -
32D LEU* 3.5 16.3 - - + +
33D PHE* 1.3 74.4 - - - +
35D TYR* 1.3 64.2 + - - +
45D PHE* 4.2 1.6 - - - -
46D LEU* 2.9 30.7 + - + +
47D SER* 3.0 32.5 + - - +
49D ASN* 5.3 1.3 - - - -
62D SER* 4.2 6.5 - - - -
71D SER* 3.1 21.2 + - - -
72D TYR* 4.4 1.6 - - - -
73D LEU* 3.7 37.3 - - + +
86D TYR* 3.9 18.8 - - + -
87D LEU 3.3 18.4 - - - -
88D CYS* 3.9 4.5 - - + -
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Residues in contact with TYR 35 (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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33D PHE* 3.5 41.8 - + + -
34D TRP* 1.3 78.0 - - - +
36D GLN* 1.3 60.2 + - - +
43D PRO* 4.3 18.2 - - + -
44D THR* 3.2 27.6 - - - +
45D PHE* 3.7 20.8 - + + +
46D LEU* 3.9 5.1 - - - +
86D TYR* 3.3 8.3 - - - +
87D LEU* 2.8 46.2 + - + +
89D ALA* 4.7 2.2 - - + -
97D LEU* 5.2 6.7 - - + +
99D TRP* 3.7 35.2 - + - -
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Residues in contact with GLN 36 (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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35D TYR* 1.3 74.7 - - - +
37D GLN* 1.3 63.3 + - - +
38D HIS* 3.7 30.8 + - + +
42D ALA 3.8 1.7 - - - +
43D PRO* 3.2 1.1 - - - +
44D THR* 2.7 51.0 + - - +
46D LEU* 3.6 28.9 - - + +
60D PHE* 4.4 10.3 - - - -
81D LYS 4.6 4.6 + - - -
82D ASP* 4.9 1.4 + - - +
84D ALA* 4.1 8.9 - - + +
85D SER 3.6 3.1 - - - -
86D TYR* 3.1 32.8 + - + -
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Residues in contact with GLN 37 (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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35D TYR 4.2 0.2 - - - -
36D GLN* 1.3 74.9 - - - +
38D HIS* 1.3 66.1 + - - +
39D ALA* 3.8 0.9 + - - -
40D GLY 5.6 1.0 - - - +
41D GLU 2.7 30.7 + - - +
42D ALA 4.2 1.1 - - - -
43D PRO* 3.9 28.3 - - + +
84D ALA* 3.9 2.5 - - - -
85D SER* 2.8 48.1 + - - +
87D LEU* 3.8 25.7 - - + +
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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