Contacts of the strand formed by residues 38 - 45 (chain M) in PDB entry 5C3I
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 38 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4M VAL* 4.0 25.6 - - + -
28M PHE* 4.0 25.6 - - + -
34M LEU* 3.7 21.8 - - + -
37M ASP* 1.3 71.7 - - - +
39M GLU* 1.3 60.3 + - - +
40M TRP* 3.9 18.0 - - + +
60M VAL 3.7 1.0 - - - +
61M LEU* 3.5 4.1 - - - -
62M VAL* 2.7 38.5 + - + +
65M VAL* 4.2 6.7 - - + +
99M CYS* 3.8 20.6 - - - -
100M THR 3.5 1.1 - - - -
101M TYR* 3.6 31.9 - - + -
106M PHE* 3.9 8.3 - - + -
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Residues in contact with GLU 39 (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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51J ILE* 5.4 0.9 - - + -
37M ASP 4.1 0.9 - - - +
38M LEU* 1.3 71.2 - - - +
40M TRP* 1.3 64.4 + - - +
41M LYS* 3.3 31.2 + - + +
59M SER* 3.6 17.3 + - - +
60M VAL 3.3 4.0 - - - +
61M LEU* 3.6 21.6 - - + +
98M THR 3.8 0.7 - - - +
99M CYS* 3.2 3.2 - - - -
100M THR* 2.8 59.4 + - - +
103M GLY* 5.6 3.6 + - - -
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Residues in contact with TRP 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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4M VAL* 5.5 1.6 - - + -
6M VAL* 4.1 20.9 - - + -
26M ILE* 3.6 39.7 - - + -
28M PHE* 3.8 26.8 - + + -
38M LEU* 3.9 29.7 - - + +
39M GLU* 1.3 73.7 - - - +
41M LYS* 1.3 62.1 + - - +
59M SER* 3.4 4.9 + - - -
60M VAL* 2.8 43.4 + - + +
62M VAL* 4.0 17.0 - - + +
72M PHE* 3.7 24.0 - + - -
74M PHE* 3.3 23.1 - - + -
97M ILE* 4.2 10.1 - - + -
98M THR 3.4 9.6 - - - -
99M CYS* 3.5 33.2 - - + -
106M PHE* 5.6 1.3 - + - -
107M ILE* 5.1 2.2 - - + -
109M VAL* 6.5 0.7 - - + -
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Residues in contact with LYS 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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39M GLU* 3.3 25.2 + - + +
40M TRP* 1.3 78.2 - - - +
42M ILE* 1.3 65.2 + - - +
43M ILE* 4.1 16.4 - - + -
56M VAL* 4.0 25.7 - - + +
58M ASP 3.7 4.9 - - - +
59M SER* 3.7 21.6 + - - +
74M PHE* 4.1 0.2 - - - -
96M LEU 3.6 0.5 - - - +
97M ILE* 3.4 6.2 - - - +
98M THR* 2.8 52.6 + - - +
100M THR* 5.7 5.6 - - + -
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Residues in contact with ILE 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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22M PHE* 5.1 1.1 - - + -
24M PHE* 3.6 32.1 - - + -
41M LYS* 1.3 74.9 - - - +
43M ILE* 1.3 63.0 + - - +
56M VAL* 3.6 3.1 - - - +
57M LEU* 2.8 50.9 + - + +
58M ASP 3.4 8.0 + - - +
74M PHE* 3.5 39.9 - - + -
76M ALA* 3.5 30.1 - - + +
95M VAL* 4.0 16.8 - - + -
96M LEU 3.3 7.6 - - - +
97M ILE* 4.7 4.9 - - + -
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Residues in contact with ILE 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 LYS* 4.5 11.4 - - + -
42M ILE* 1.3 76.4 - - - +
44M TYR* 1.3 64.3 + - - +
45M VAL 3.9 0.5 + - - -
54M ASP* 3.9 30.3 - - + +
55M GLN 3.5 8.3 - - - +
56M VAL* 4.1 19.1 - - + -
95M VAL* 3.5 6.1 - - - +
96M LEU* 2.7 62.5 + - + +
98M THR* 4.0 32.8 - - + +
105M GLU* 5.8 0.2 - - - +
108M ARG* 4.8 7.9 - - - +
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Residues in contact with TYR 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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18M PHE* 4.6 8.3 - + - -
22M PHE* 4.0 14.8 - + - -
42M ILE 4.1 0.6 + - - -
43M ILE* 1.3 73.4 - - - +
45M VAL* 1.3 73.6 + - - +
46M GLY* 3.2 11.3 + - - -
54M ASP* 3.4 2.1 - - - -
55M GLN* 2.8 40.9 + - + +
57M LEU* 3.8 26.2 - - + +
79M PRO* 3.7 32.3 - - + -
84M ILE* 4.2 16.8 - - + +
89M ALA* 6.0 1.0 - - - -
93M THR* 3.4 20.8 - - + +
94M VAL 4.2 0.9 - - - -
95M VAL* 3.6 23.3 - - + +
113M VAL* 4.6 5.8 - - + -
115M ASN* 3.2 28.7 + - - -
137M ARG* 6.0 0.9 - - - -
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Residues in contact with VAL 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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43M ILE* 5.3 0.2 - - + -
44M TYR* 1.3 77.1 - - - +
46M GLY* 1.3 60.9 + - - +
47M SER 3.4 28.0 - - - +
48M ALA* 4.3 1.8 - - - +
54M ASP* 3.9 7.9 - - - +
93M THR* 2.6 30.9 + - - +
94M VAL* 3.0 45.0 + - + +
96M LEU* 4.2 15.5 - - + -
126N LEU* 4.3 7.0 - - + -
129N ARG* 3.8 32.8 - - + +
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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