Contacts of the strand formed by residues 39 - 45 (chain T) in PDB entry 1UW9
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 39 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73B GLY 3.4 26.5 - - - +
74B LEU* 4.9 1.6 - - - -
37T GLY 5.0 1.1 - - - +
38T TRP* 1.3 72.9 - - - +
40T PRO* 1.3 64.1 - - - +
79T PRO* 3.7 28.9 - - + -
80T MET 3.7 9.6 - - - +
81T PHE* 3.7 24.9 - - + +
109T ALA* 3.0 4.6 - - - -
110T PHE* 2.8 59.8 + - + +
112T ASN* 4.2 17.0 - - + +
1142T EDO 3.5 20.9 - - - +
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Residues in contact with PRO 40 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33T ILE* 4.0 15.9 - - + -
34T VAL* 5.5 2.2 - - + -
38T TRP 3.3 8.9 - - - +
39T ILE* 1.3 86.6 - - - +
41T CYS* 1.3 59.8 + - - +
79T PRO* 3.6 0.5 - - - +
80T MET* 2.8 58.0 + - + +
83T CYS* 4.4 10.5 - - + +
89T VAL* 3.8 38.8 - - + -
107T LEU* 4.7 3.4 - - + -
108T VAL 3.5 8.1 - - - +
109T ALA* 4.3 4.0 - - + -
1142T EDO 4.9 0.7 - - - -
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Residues in contact with CYS 41 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40T PRO* 1.3 77.5 - - - +
42T LEU* 1.3 77.8 + - - +
43T GLU* 4.9 3.6 - - - -
75T MET* 3.9 18.8 - - - -
76T TRP 4.7 0.9 - - - -
78T LEU 4.3 3.8 - - - -
79T PRO* 3.7 31.0 - - + -
80T MET* 5.2 4.5 - - - -
107T LEU* 3.7 5.1 - - - +
108T VAL* 2.9 40.0 + - + +
110T PHE* 3.7 27.4 - - + -
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Residues in contact with LEU 42 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41T CYS* 1.3 82.8 - - - +
43T GLU* 1.3 65.0 - - - +
75T MET 3.8 0.2 - - - -
76T TRP* 2.9 49.8 + - + -
78T LEU 5.6 0.2 + - - -
80T MET* 5.9 3.1 - - - -
89T VAL* 4.9 1.6 - - + +
92T GLU* 3.4 45.8 - - + +
93T ILE* 3.6 24.7 - - + +
96T CYS* 4.1 7.6 - - + -
105T VAL* 4.0 15.3 - - + -
106T ARG 3.6 14.6 - - - +
107T LEU* 3.9 19.3 - - + -
123T VAL* 4.4 1.3 - - + -
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Residues in contact with GLU 43 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A ARG* 2.9 35.5 + - - -
41T CYS* 4.9 4.8 - - - -
42T LEU* 1.3 80.5 - - - +
44T PHE* 1.3 61.2 + - - +
73T TRP* 3.8 20.1 + - + +
74T THR 3.2 13.5 - - - +
75T MET* 4.6 7.6 - - + +
76T TRP 4.4 0.2 - - - +
105T VAL* 3.4 5.5 - - - +
106T ARG* 2.8 74.3 + - + +
108T VAL* 3.8 23.7 - - + +
110T PHE* 4.7 1.4 - - - -
117T GLN* 4.6 2.6 - - - +
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Residues in contact with PHE 44 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3I VAL* 4.0 6.7 - - + -
6I PRO* 3.6 21.5 - - + -
7I VAL* 5.5 1.1 - - + -
43T GLU* 1.3 77.9 - - - +
45T ALA* 1.3 64.8 + - - +
73T TRP* 3.4 5.3 - - - +
74T THR* 2.9 63.0 + - + -
75T MET 3.6 17.3 - - - -
76T TRP* 3.9 24.2 - + + -
96T CYS* 4.2 8.7 - - - -
100T PHE* 3.5 48.5 - + + -
103T ALA* 4.4 6.3 - - + -
104T TYR 3.1 14.1 - - - +
105T VAL* 4.0 14.1 - - + -
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Residues in contact with ALA 45 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A LYS* 5.7 2.0 - - - +
6I PRO* 6.0 1.3 - - - -
44T PHE* 1.3 81.2 - - - +
46T GLU* 1.3 65.8 + - - +
49T LYS* 3.7 24.0 - - + +
50T ALA* 4.4 1.6 - - - -
73T TRP* 3.7 29.8 - - + -
74T THR* 5.4 1.8 - - - +
103T ALA* 3.4 5.5 - - - +
104T TYR* 2.8 33.8 + - - +
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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