Contacts of the strand formed by residues 39 - 45 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37M GLY 4.9 1.6 - - - +
38M TRP* 1.3 70.5 - - - +
40M PRO* 1.3 63.6 - - - +
79M PRO* 3.6 30.3 - - + -
80M MET 3.7 17.5 - - - +
81M PHE* 3.7 18.2 - - + -
109M ALA* 3.0 5.6 - - - -
110M PHE* 2.8 57.3 + - + +
112M ASN* 4.2 16.2 - - + +
1142M EDO 3.4 20.0 - - - +
73V GLY 3.4 26.7 - - - +
74V LEU* 4.9 1.3 - - - -
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Residues in contact with PRO 40 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33M ILE* 3.9 17.0 - - + -
34M VAL* 5.4 2.5 - - + -
38M TRP 3.2 9.8 - - - +
39M ILE* 1.3 85.8 - - - +
41M CYS* 1.3 59.0 + - - +
79M PRO* 3.5 0.5 - - - +
80M MET* 2.8 61.8 + - + +
83M CYS* 4.4 12.1 - - + +
89M VAL* 3.7 38.1 - - + -
107M LEU* 4.6 2.5 - - + -
108M VAL 3.5 9.0 - - - +
109M ALA* 4.3 3.4 - - + -
1142M EDO 5.4 0.2 - - - +
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Residues in contact with CYS 41 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40M PRO* 1.3 76.6 - - - +
42M LEU* 1.3 76.8 + - - +
43M GLU* 4.8 4.0 - - - -
75M MET* 4.0 17.7 - - - -
76M TRP 4.8 0.4 - - - -
78M LEU 4.4 3.1 - - - -
79M PRO* 3.8 32.5 - - + -
80M MET* 5.3 4.0 - - - -
107M LEU* 3.6 5.5 - - - +
108M VAL* 2.9 39.6 + - + +
110M PHE* 3.6 27.6 - - + -
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Residues in contact with LEU 42 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41M CYS* 1.3 82.1 - - - +
43M GLU* 1.3 66.6 + - - +
75M MET 3.8 0.2 - - - -
76M TRP* 2.9 49.4 + - + -
78M LEU 5.7 0.2 + - - -
80M MET* 5.9 3.5 - - - -
89M VAL* 4.7 1.8 - - + +
92M GLU* 3.5 46.2 - - + +
93M ILE* 3.5 25.1 - - + +
96M CYS* 4.1 7.4 - - + -
105M VAL* 4.0 14.4 - - + -
106M ARG 3.5 13.7 - - - +
107M LEU* 3.9 19.5 - - + -
123M VAL* 4.5 1.6 - - + -
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Residues in contact with GLU 43 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41M CYS* 4.8 5.2 - - - -
42M LEU* 1.3 80.8 - - - +
44M PHE* 1.3 62.5 + - - +
72M TYR* 6.1 0.2 - - - -
73M TRP* 3.7 19.5 + - + +
74M THR 3.2 13.2 - - - +
75M MET* 4.7 8.0 - - + +
76M TRP 4.4 0.2 - - - +
105M VAL* 3.4 4.9 - - - +
106M ARG* 2.8 71.0 + - + +
108M VAL* 3.8 23.8 - - + +
110M PHE* 4.8 1.2 - - - -
117M GLN* 4.7 2.3 - - - +
187O ARG* 3.0 34.5 + - - -
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Residues in contact with PHE 44 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43M GLU* 1.3 79.4 - - - +
45M ALA* 1.3 66.0 + - - +
46M GLU 5.5 0.2 - - - -
73M TRP* 3.4 4.2 - - - +
74M THR* 2.8 64.4 + - + -
75M MET 3.7 16.4 - - - -
76M TRP* 3.9 23.8 - + + -
96M CYS* 4.2 9.4 - - - -
100M PHE* 3.5 44.0 - + - -
103M ALA* 4.4 6.1 - - + -
104M TYR 3.1 14.4 - - - +
105M VAL* 4.0 13.7 - - + -
3T VAL* 4.2 6.5 - - + -
6T PRO* 3.5 26.5 - - + -
7T VAL* 5.3 1.3 - - + -
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Residues in contact with ALA 45 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44M PHE* 1.3 80.3 - - - +
46M GLU* 1.3 66.0 + - - +
49M LYS* 3.8 21.5 - - + +
50M ALA* 4.4 0.7 - - - -
73M TRP* 3.6 34.3 - - + -
74M THR* 5.5 1.3 - - - -
103M ALA* 3.5 5.6 - - - +
104M TYR* 2.8 32.9 + - - +
227O LYS* 5.7 1.6 - - - +
6T PRO* 6.2 1.3 - - - -
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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