Contacts of the strand formed by residues 18 - 28 (chain I) in PDB entry 1MWA
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 18 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14I ARG* 2.9 17.5 + - - +
15I PRO* 4.5 2.3 - - - +
16I GLY 3.6 2.0 - - - +
17I LEU* 1.3 80.9 - - - +
19I GLU* 1.3 67.2 + - - -
20I PRO* 4.6 0.7 - - - +
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Residues in contact with GLU 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14I ARG* 3.8 16.5 + - - -
18I GLY* 1.3 77.5 - - - -
20I PRO* 1.3 80.3 - - + +
75I ARG* 2.6 48.4 + - - +
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Residues in contact with PRO 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11I ALA* 4.8 5.6 - - + -
12I VAL 3.1 20.0 - - - +
13I SER* 4.0 9.0 - - - -
14I ARG* 4.3 0.9 - - - +
18I GLY 4.6 0.9 - - - +
19I GLU* 1.3 98.0 - - + +
21I ARG* 1.3 64.3 + - - +
22I TYR* 3.9 1.1 + - - -
38I SER* 4.8 1.4 + - - +
39I ASP* 5.0 1.2 - - - +
71I GLU* 4.4 10.2 - - - +
75I ARG* 3.8 33.3 + - + +
78I LEU* 3.3 32.3 - - + -
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Residues in contact with ARG 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10I THR* 3.4 1.8 - - - +
11I ALA* 3.0 27.0 - - - +
12I VAL* 2.9 24.1 + - + -
14I ARG* 2.9 39.3 - - - +
20I PRO* 1.3 73.4 - - - +
22I TYR* 1.3 64.3 + - - +
23I MET* 3.0 30.8 - - + +
37I ASP* 3.5 22.0 + - - +
39I ASP* 3.4 23.4 + - - +
53M ASP* 5.6 2.8 + - - -
54M MET* 6.0 2.4 - - - +
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Residues in contact with TYR 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9I VAL* 3.4 26.2 - - + +
10I THR 3.6 4.3 - - - -
11I ALA* 3.9 17.0 - - + -
20I PRO 3.9 0.6 + - - +
21I ARG* 1.3 76.1 - - - +
23I MET* 1.3 63.0 - - - +
24I GLU* 3.6 27.4 + - + -
36I PHE* 3.7 20.4 - + - -
37I ASP* 2.7 22.8 - - - +
38I SER* 2.8 36.4 + - - +
67I ALA 3.6 13.2 - - - -
70I ASN* 3.5 17.5 + - - +
71I GLU* 3.6 37.2 - - + +
74I PHE* 3.4 33.3 - + + -
2Q GLN* 5.4 0.2 + - - -
5Q PHE* 5.4 0.3 - - - -
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Residues in contact with MET 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8I PHE 4.2 0.9 - - - +
9I VAL* 4.0 1.0 - - - +
10I THR* 2.9 58.4 + - + +
21I ARG* 3.0 49.1 - - - +
22I TYR* 1.3 73.9 - - - +
24I GLU* 1.3 66.3 + - - +
25I VAL* 6.0 0.7 - - + -
35I ARG* 4.1 13.0 - - - +
36I PHE 2.8 13.5 - - - +
37I ASP* 3.0 32.3 - - + +
53M ASP* 5.4 3.1 - - - +
54M MET* 4.0 38.4 - - + +
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Residues in contact with GLU 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7I TYR* 4.3 3.5 - - - -
8I PHE 4.0 2.9 - - - +
9I VAL* 3.9 11.5 - - + +
22I TYR* 3.6 32.1 + - + -
23I MET* 1.3 79.3 - - - +
25I VAL* 1.3 73.7 + - - +
34I VAL 4.0 1.3 - - - -
35I ARG* 3.0 5.4 - - - -
36I PHE* 2.5 32.9 + - + +
45I TYR* 2.6 39.4 + - + +
67I ALA* 3.6 20.8 - - - +
70I ASN* 4.1 4.9 + - - -
2Q GLN* 3.1 30.3 - - - +
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Residues in contact with VAL 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7I TYR* 3.8 4.0 - - - -
8I PHE* 3.0 51.8 + - + +
23I MET* 5.5 1.6 - - + -
24I GLU* 1.3 81.0 - - - +
26I GLY* 1.3 63.1 + - - +
27I TYR* 3.8 15.7 + - + +
32I GLU* 3.1 15.9 - - - +
34I VAL 3.1 5.4 - - - -
35I ARG* 2.9 48.7 - - - +
54M MET 5.0 2.7 - - - +
55M SER* 5.4 3.8 - - - +
56M PHE* 5.9 0.9 - - + -
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Residues in contact with GLY 26 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6I ARG 3.5 2.5 - - - -
7I TYR* 3.4 26.8 - - - -
25I VAL* 1.3 74.0 - - - +
27I TYR* 1.3 60.4 + - - -
32I GLU* 3.5 6.1 - - - +
33I PHE* 3.0 40.5 + - - -
34I VAL* 3.1 13.3 + - - +
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Residues in contact with TYR 27 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4I SER* 4.4 0.7 + - - -
5I LEU* 3.7 1.5 + - - +
6I ARG* 2.6 48.0 + - + +
8I PHE* 3.0 45.8 - + + -
25I VAL* 3.8 13.9 - - + +
26I GLY* 1.3 72.3 - - - -
28I VAL* 1.3 61.1 + - - +
29I ASP 3.3 6.3 + - - -
30I ASP* 3.2 33.3 + - - +
32I GLU* 3.3 43.7 + - + +
33I PHE* 3.8 1.0 - - - -
55M SER* 3.4 29.8 + - - -
56M PHE 5.2 4.0 - - - -
63M TYR* 4.5 6.9 + - - -
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Residues in contact with VAL 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4I SER 3.7 9.2 - - - +
5I LEU* 3.3 26.7 - - + -
26I GLY 4.0 1.0 + - - -
27I TYR* 1.3 68.7 - - - +
29I ASP* 1.3 72.7 + - - +
31I THR* 3.1 28.6 + - - +
33I PHE* 3.6 26.2 - - + -
51I TRP* 4.8 1.1 - - + -
168I LEU* 5.0 0.2 - - + -
171I TYR* 3.7 12.8 - - + -
172I LEU* 3.4 20.6 - - + -
179I LEU* 3.3 32.3 - - + +
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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