Contacts of the strand formed by residues 37 - 44 (chain D) in PDB entry 4U0Q
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 ILE 37 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30D VAL* 3.8 28.0 - - + -
31D GLU 3.3 15.7 - - - +
32D ASP* 3.7 32.1 - - + +
33D LEU* 4.7 1.3 - - - +
35D SER 5.4 0.2 - - - +
36D LYS* 1.3 72.0 - - - +
38D LEU* 1.3 57.6 + - - +
39D LEU* 4.0 7.8 + - + -
74D PHE 3.7 0.5 - - - +
75D LYS* 3.5 2.4 - - - -
76D VAL* 2.7 47.5 + - + +
81D GLN* 3.7 36.3 - - + +
101D LEU* 4.3 7.4 - - + -
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Residues in contact with LEU 38 (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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499A TYR* 3.2 33.9 - - + +
29D THR 3.7 0.5 - - - +
30D VAL* 3.4 5.4 - - - +
31D GLU* 2.7 40.6 + - + +
33D LEU* 3.7 21.6 - - + +
37D ILE* 1.3 71.3 - - - +
39D LEU* 1.3 65.1 + - - +
40D THR* 4.1 6.6 + - - +
73D GLU* 3.8 28.3 - - + +
74D PHE 3.6 30.3 - - - +
75D LYS* 3.8 20.6 - - + +
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Residues in contact with LEU 39 (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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29D THR 3.5 2.7 - - - -
30D VAL* 3.7 26.0 - - + -
37D ILE* 4.3 10.1 - - + -
38D LEU* 1.3 71.5 - - - +
40D THR* 1.3 61.8 + - - +
55D TRP* 3.6 16.6 - - + -
73D GLU* 3.3 5.9 - - - +
74D PHE* 2.8 42.8 + - + +
76D VAL* 3.7 17.0 - - + -
85D TYR* 3.6 42.6 - - + -
99D ILE* 3.7 28.7 - - + -
101D LEU* 4.4 7.4 - - + -
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Residues in contact with THR 40 (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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499A TYR* 4.4 3.4 + - - +
27D PHE 4.3 1.3 - - - -
28D THR* 3.4 5.4 - - - -
29D THR* 2.8 58.7 + - - +
31D GLU* 5.4 0.3 - - - +
38D LEU* 4.2 12.5 + - - +
39D LEU* 1.3 75.0 - - - +
41D CYS* 1.3 68.2 + - - +
55D TRP* 4.4 0.2 - - - -
71D LYS* 3.6 35.4 - - + +
72D THR 3.4 10.1 - - - +
73D GLU* 3.7 20.6 - - + +
99D ILE* 4.2 1.9 - - - +
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Residues in contact with CYS 41 (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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26D VAL* 4.0 4.0 - - + -
27D PHE 3.4 3.4 - - - -
28D THR* 4.0 15.0 - - - -
40D THR* 1.3 80.7 - - - +
42D SER* 1.3 60.7 + - - +
55D TRP* 3.9 6.1 - - - -
71D LYS* 3.3 5.0 - - - +
72D THR* 2.8 45.9 + - + +
87D CYS* 2.0 52.5 - - + -
89D PHE* 3.5 9.9 - - + -
97D ALA* 4.2 0.4 - - - -
99D ILE* 4.1 7.4 - - - -
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Residues in contact with SER 42 (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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25D THR 3.5 1.4 - - - +
26D VAL* 3.3 3.3 - - - +
27D PHE* 2.8 52.1 + - - +
41D CYS* 1.3 73.7 - - - +
43D LEU* 1.3 60.2 + - - +
44D ASN* 3.7 16.9 + - - -
70D GLN* 3.3 9.7 + - - +
71D LYS* 4.0 21.8 - - - +
89D PHE* 4.1 1.3 - - - -
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Residues in contact with LEU 43 (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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350C PHE* 4.1 4.0 - - + -
24D GLY* 4.5 0.2 - - - -
25D THR 3.7 15.0 - - - +
26D VAL* 3.9 20.4 - - + +
42D SER* 1.3 69.5 - - - +
44D ASN* 1.3 75.4 + - - +
46D SER* 3.7 27.1 + - - -
50D VAL* 4.8 3.1 - - + -
70D GLN* 2.8 39.5 + - + +
89D PHE* 3.5 30.7 - - + -
94D MET* 3.5 47.1 - - - +
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Residues in contact with ASN 44 (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 GLY* 3.3 1.2 - - - -
25D THR 2.9 38.2 + - - +
27D PHE* 3.3 32.1 - - + +
42D SER* 3.7 16.1 + - - -
43D LEU* 1.3 83.2 - - - +
45D ASP* 1.3 76.3 + - - +
46D SER 3.3 3.3 + - - -
70D GLN* 5.1 1.9 - - - +
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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