Contacts of the strand formed by residues 52 - 66 (chain B) in PDB entry 1MRW
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 GLY 52 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A ILE* 4.4 0.5 - - - +
51A GLY* 3.4 12.1 + - - -
81A PRO* 5.3 3.4 - - - +
47B ILE 3.9 0.7 - - - +
49B GLY 2.8 33.6 + - - -
50B ILE 3.5 0.4 + - - -
51B GLY* 1.3 79.5 - - - +
53B PHE* 1.3 67.1 + - - -
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Residues in contact with PHE 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A PRO* 6.4 2.5 - - + -
46B MET* 4.4 29.3 - - + +
47B ILE* 3.2 12.1 - - - +
48B GLY* 3.5 28.7 - - - -
52B GLY* 1.3 79.1 - - - -
54B ILE* 1.3 64.6 + - - +
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Residues in contact with ILE 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ILE* 3.5 38.1 - - + +
51A GLY* 4.2 10.3 - - - +
32B VAL* 5.8 0.4 - - + -
45B LYS 3.6 0.5 - - - +
46B MET* 3.3 11.4 - - - +
47B ILE* 3.0 46.3 + - + +
53B PHE* 1.3 80.8 - - - +
55B LYS* 1.3 62.0 + - - +
56B VAL* 3.8 20.9 - - + -
79B PRO* 3.8 35.4 - - + +
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Residues in contact with LYS 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B PRO* 6.4 3.6 - - + -
45B LYS 3.5 5.8 - - - +
46B MET* 3.3 27.4 - - + -
54B ILE* 1.3 74.5 - - - +
56B VAL* 1.3 65.7 + - - +
79B PRO* 4.2 15.8 - - - +
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Residues in contact with VAL 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B VAL* 4.7 6.3 - - + -
42B TRP* 4.6 2.0 - - - -
43B LYS 4.0 1.0 - - - +
44B PRO* 4.0 3.5 - - - +
45B LYS* 2.9 50.4 + - + +
47B ILE* 3.9 15.3 - - + -
54B ILE* 3.8 24.2 - - + -
55B LYS* 1.3 82.5 - - - +
57B ARG* 1.3 62.6 + - - +
76B LEU* 3.8 32.3 - - + -
77B VAL 3.5 16.4 - - - +
78B GLY* 4.3 9.0 - - - +
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Residues in contact with ARG 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B GLU* 2.9 42.0 + - - -
36B MET 3.7 8.7 + - - -
42B TRP* 3.4 50.2 - - + +
56B VAL* 1.3 74.5 - - - +
58B GLN* 1.3 61.2 + - - +
59B TYR* 2.8 36.4 + - + -
75B VAL 3.8 0.9 - - - +
76B LEU* 3.1 5.9 - - - -
77B VAL* 2.8 55.9 + - - +
78B GLY* 5.5 0.8 - - - -
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Residues in contact with GLN 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B ARG 4.3 0.3 - - - +
42B TRP* 3.2 6.8 - - - -
43B LYS* 2.8 68.6 + - - +
44B PRO 4.4 4.6 + - - -
45B LYS* 3.8 34.6 - - + +
56B VAL 3.9 0.2 + - - -
57B ARG* 1.3 72.7 - - - +
59B TYR* 1.3 61.8 + - - +
60B ASP* 3.0 23.9 + - - +
74B THR* 3.6 19.0 + - + +
76B LEU* 3.5 13.5 - - + +
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Residues in contact with TYR 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B LEU* 3.7 43.9 + - + -
39B PRO 3.6 17.7 - - - -
40B GLY 3.9 10.3 - - - -
41B ARG 4.0 11.9 - - - -
42B TRP* 3.6 23.5 - + + -
57B ARG* 2.8 52.6 + - + -
58B GLN* 1.3 75.5 - - - +
60B ASP* 1.3 63.0 + - - +
62B ILE* 3.6 20.8 - - + +
74B THR* 3.3 2.6 - - - +
75B VAL 2.9 36.9 + - - +
77B VAL* 3.8 18.2 - - + -
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Residues in contact with ASP 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B ARG 5.1 2.4 + - - -
43B LYS* 3.1 30.7 + - - -
58B GLN* 3.0 19.4 + - - +
59B TYR* 1.3 73.1 - - - +
61B GLN* 1.3 76.0 + - + +
62B ILE* 3.2 11.8 + - - +
74B THR* 2.8 28.4 + - - +
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Residues in contact with GLN 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B ASP* 1.3 80.3 - - + +
62B ILE* 1.3 63.3 + - - +
63B ILE* 3.8 4.5 + - - +
72B ILE* 3.7 26.1 - - + +
73B GLY* 3.3 14.4 + - - +
74B THR* 4.8 0.2 + - - -
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Residues in contact with ILE 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ILE* 4.2 16.4 - - + -
38B LEU* 4.4 12.3 - - + -
39B PRO* 4.3 28.7 - - + +
59B TYR* 3.6 39.3 - - + +
60B ASP 3.8 9.6 - - - +
61B GLN* 1.3 74.0 - - - +
63B ILE* 1.3 73.9 + - - +
64B ILE* 3.6 5.5 + - + +
72B ILE* 3.2 3.7 - - - -
73B GLY 2.7 35.6 + - - +
75B VAL* 3.8 20.4 - - + -
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Residues in contact with ILE 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B LYS 4.3 0.5 - - - +
15B ILE* 4.0 13.5 - - - +
16B GLY 4.5 2.9 + - - -
61B GLN 3.8 4.0 + - - +
62B ILE* 1.3 83.2 - - - +
64B ILE* 1.3 65.3 + - - +
70B LYS* 4.4 21.5 - - + +
71B ALA 3.6 8.3 - - - +
72B ILE* 4.1 26.0 - - + -
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Residues in contact with ILE 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ILE* 4.1 6.7 - - + -
14B LYS 3.4 5.6 - - - +
15B ILE* 3.4 38.8 - - + -
31B THR* 5.0 3.6 - - + -
62B ILE* 4.0 10.1 - - + +
63B ILE* 1.3 80.6 - - - +
65B GLU* 1.3 61.7 + - - +
66B ILE* 3.4 26.9 - - + +
70B LYS* 4.6 0.9 - - - -
71B ALA* 2.7 58.0 + - + +
75B VAL* 4.9 7.0 - - + -
85B ILE* 4.2 9.4 - - + -
89B LEU* 4.0 26.9 - - + -
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Residues in contact with GLU 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B THR 4.3 0.2 - - - +
13B ILE* 3.1 9.4 - - - +
14B LYS* 2.8 69.1 + - + +
64B ILE* 1.3 73.2 - - - +
66B ILE* 1.3 64.2 + - - +
67B CYS 4.1 0.6 + - - +
68B GLY* 3.7 35.6 + - - +
69B HIS 3.3 7.4 - - - +
70B LYS* 3.7 35.9 + - + +
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Residues in contact with ILE 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A PHE* 4.9 1.5 - - + -
11B VAL* 4.1 20.6 - - + -
13B ILE* 3.3 23.3 - - + -
24B LEU* 4.3 12.1 - - + -
64B ILE* 3.4 35.2 - - + +
65B GLU* 1.3 73.0 - - - +
67B CYS* 1.3 75.1 + - + +
68B GLY 2.9 0.2 - - - -
69B HIS* 2.6 34.6 + - - +
71B ALA* 5.0 3.4 - - + -
85B ILE* 3.9 18.2 - - + -
89B LEU* 5.2 4.3 - - + -
93B ILE* 4.3 30.7 - - + -
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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