Contacts of the strand formed by residues 47 - 55 (chain M) in PDB entry 2W4G
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 PHE 47 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39M PHE* 5.4 0.4 - - + -
40M VAL* 3.1 25.1 - - - +
41M VAL* 4.2 13.5 - - + -
42M HIS 4.6 0.2 - - - +
45M GLU 4.6 1.3 - - - -
46M SER* 1.3 86.2 - - - +
48M VAL* 1.3 53.9 + - - +
78M PHE* 3.2 32.8 - + - -
99M GLU* 3.9 30.5 - - + -
100M PRO* 3.6 39.0 - - + -
103M LEU* 4.8 4.9 - - + -
104M TYR* 2.5 41.1 + - + -
688M HIS* 4.1 7.4 + - - -
692M LEU* 4.1 21.1 - - + -
696M ARG* 5.2 0.4 - - - -
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Residues in contact with VAL 48 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39M PHE* 3.8 2.3 - - - -
40M VAL* 2.9 37.5 + - + +
42M HIS* 3.4 34.5 - - + +
45M GLU* 5.0 13.2 - - + +
47M PHE* 1.3 76.5 - - - +
49M LYS* 1.4 76.8 + - + +
64M THR* 4.3 17.5 - - + +
65M GLU* 4.3 18.6 - - + +
104M TYR* 3.1 11.9 - - - +
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Residues in contact with LYS 49 (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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38M VAL 3.7 10.3 - - - +
39M PHE* 3.7 35.2 - - + -
40M VAL* 5.5 2.0 - - - -
48M VAL* 1.4 84.3 - - + +
50M GLY* 1.3 60.1 + - - +
63M LYS 4.7 0.2 - - - -
64M THR* 3.6 3.6 - - - +
65M GLU* 3.2 54.5 + - + +
80M MET* 3.9 28.2 - - + +
104M TYR* 4.3 15.9 - - + +
108M GLU* 3.3 25.3 + - - -
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Residues in contact with GLY 50 (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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37M SER* 3.9 2.6 - - - -
38M VAL* 2.7 35.1 + - - +
39M PHE* 4.9 0.2 - - - +
40M VAL* 5.3 2.0 - - - +
49M LYS* 1.3 77.6 - - - +
51M THR* 1.3 64.8 + - - -
62M VAL* 3.6 8.1 - - - -
63M LYS 3.2 16.6 - - - -
64M THR* 4.2 3.1 - - - -
65M GLU* 5.4 2.9 - - - -
80M MET* 5.6 0.5 - - - +
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Residues in contact with THR 51 (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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36M SER* 3.7 21.1 - - - +
37M SER* 4.9 4.4 - - - +
50M GLY* 1.3 73.7 - - - -
52M ILE* 1.3 73.0 + - - +
53M GLN* 3.4 10.0 + - - +
62M VAL* 2.6 24.0 - - - +
63M LYS* 2.9 26.1 + - - -
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Residues in contact with ILE 52 (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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35M LYS 4.3 5.6 - - - +
36M SER* 2.8 41.5 + - - +
38M VAL* 3.3 42.4 - - + -
51M THR* 1.3 84.8 - - - +
53M GLN* 1.3 66.6 + - - +
54M SER 3.3 22.4 - - - +
55M LYS* 5.2 8.7 - - + -
60M VAL* 4.0 16.8 - - + -
61M THR 4.0 1.8 - - - -
62M VAL* 3.7 14.6 - - + -
77M VAL* 5.0 2.5 - - + -
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Residues in contact with GLN 53 (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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51M THR* 4.3 11.1 + - - +
52M ILE* 1.3 80.2 + - - +
54M SER* 1.3 69.1 + - - +
61M THR* 3.0 15.8 + - - +
62M VAL 4.2 2.0 - - - -
63M LYS* 3.8 49.9 + - + +
69M THR* 4.9 9.8 - - + +
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Residues in contact with SER 54 (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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52M ILE* 3.3 19.3 - - - +
53M GLN* 1.3 81.3 - - - +
55M LYS* 1.3 68.9 + - - +
56M GLU* 5.3 2.8 - - - +
60M VAL* 4.3 1.0 - - - +
61M THR* 2.4 42.1 + - - +
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Residues in contact with LYS 55 (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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52M ILE* 5.2 7.4 - - + -
54M SER* 1.3 83.3 - - - +
56M GLU* 1.3 59.2 + - - +
57M GLY* 3.2 14.0 + - - +
58M GLY 5.6 1.1 - - - +
59M LYS 3.9 11.2 - - - +
60M VAL* 4.4 11.4 - - + +
74M GLU* 3.5 33.6 + - - +
77M VAL* 6.1 2.6 - - - +
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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