Contacts of the strand formed by residues 32 - 38 (chain D) in PDB entry 3UTS
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 TYR 32 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A GLN* 4.1 15.7 + - - -
158A ALA* 6.0 1.4 - - - +
5C PRO* 6.1 0.7 - - + -
31D GLN* 1.3 97.6 - - + +
33D PHE* 1.3 61.4 + - - +
34D MET* 4.1 3.1 - - + -
49D TYR* 5.7 2.2 - + - -
50D THR 3.6 7.2 - - - -
51D TYR* 3.4 34.8 - + + -
91D MET* 2.9 31.4 - - - +
92D ARG* 3.2 46.4 + - + -
93D GLY 3.9 11.0 - - - -
94D ASP* 4.8 5.0 - - + +
101E ALA* 4.6 11.0 - - - -
103E ASN* 3.7 32.1 - - - +
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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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25D TYR* 3.3 42.2 - + - -
30D PHE* 3.6 31.4 - - + -
31D GLN* 3.5 22.2 - - - -
32D TYR* 1.3 78.4 - - - +
34D MET* 1.3 60.1 + - - +
35D TRP* 5.4 2.6 - - - -
49D TYR* 3.4 0.5 - - - -
50D THR* 2.7 53.0 + - - +
52D SER 4.2 6.5 - - - -
65D VAL* 4.0 21.3 - - + -
67D LYS* 4.2 8.1 - - - -
72D ILE* 2.8 37.9 - - + -
90D ALA 3.5 2.7 - - - +
91D MET* 3.6 11.7 - - + -
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Residues in contact with MET 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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32D TYR* 4.1 5.4 - - + +
33D PHE* 1.3 88.7 - - - +
35D TRP* 1.3 69.0 + - - +
36D TYR* 4.0 23.1 - - + +
46D LEU* 3.7 13.2 - - + -
48D MET 3.1 15.5 - - - +
49D TYR* 3.4 18.6 - - + -
50D THR 4.4 0.4 - - - +
89D CYS* 3.4 5.5 - - - +
90D ALA* 2.9 45.4 + - + +
91D MET* 4.9 1.8 - - - -
92D ARG* 5.8 0.2 - - - -
99D LEU* 5.2 7.2 - - + -
103E ASN* 2.9 53.8 - - + +
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Residues in contact with TRP 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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6D GLN* 3.9 18.6 - - - -
21D LEU* 3.9 12.1 - - + -
22D ASN* 3.6 26.0 - - - -
23D CYS* 3.7 11.4 - - - -
33D PHE 5.4 1.8 - - - -
34D MET* 1.3 77.7 + - - +
36D TYR* 1.3 63.7 + - - +
46D LEU* 3.7 2.8 - - - +
47D LEU* 2.8 30.5 + - + +
48D MET* 2.9 16.6 + - + +
50D THR* 5.9 0.2 - - - -
63D ALA* 4.5 16.6 - - + +
72D ILE* 3.4 35.8 - - + +
73D SER* 3.8 7.5 + - - -
74D LEU* 3.5 55.5 - - + +
87D TYR* 4.7 4.9 - - + -
88D LEU 3.4 22.0 - - - -
89D CYS* 3.8 15.7 - - + -
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Residues in contact with TYR 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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34D MET* 4.0 12.7 - - + +
35D TRP* 1.3 79.4 - - - +
37D ARG* 1.3 60.6 + - - +
44D PRO* 4.0 24.5 - - + -
45D GLU 3.4 6.7 - - - -
46D LEU* 3.6 36.0 - - + +
47D LEU* 4.3 2.0 - - - -
87D TYR* 3.5 10.4 - - - -
88D LEU* 2.8 42.9 + - + +
90D ALA* 4.0 16.8 - - + -
99D LEU* 3.6 19.1 - - + +
101D PHE* 3.7 30.7 - + - -
103E ASN 4.1 13.7 + - - -
105E GLN* 4.8 5.9 + - + +
107E PHE* 3.9 27.2 - + - -
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Residues in contact with ARG 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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36D TYR* 1.3 74.3 - - - +
38D GLN* 1.3 63.8 + - - +
39D TYR* 3.3 36.3 + - + -
44D PRO* 3.4 1.5 - - - +
45D GLU* 2.8 59.5 + - + +
47D LEU* 3.7 27.9 - - + +
61D PHE* 4.1 20.2 - - - -
82D SER 4.9 0.4 + - - -
83D ASP* 4.2 14.7 + - - +
85D ALA* 4.0 11.0 - - + -
86D THR 3.6 2.9 - - - -
87D TYR* 3.6 33.0 + - + -
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Residues in contact with GLN 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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37D ARG* 1.3 75.7 - - - +
39D TYR* 1.3 64.1 + - - +
40D SER 4.0 0.5 + - - -
41D ARG 6.0 0.2 - - - +
42D LYS 3.1 27.4 + - - +
43D GLY* 3.8 7.9 - - - +
44D PRO* 4.3 13.5 - - + +
85D ALA* 3.4 3.1 - - - +
86D THR* 2.8 51.5 + - - +
88D LEU* 3.8 18.2 - - + +
37E GLN* 2.6 47.0 + - - -
91E PHE* 4.2 10.7 - - - -
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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