Contacts of the strand formed by residues 44 - 53 (chain A) in PDB entry 1MPG
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 TYR 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A ALA* 3.2 4.2 - - - +
41A VAL 2.8 39.2 + - - +
43A GLU* 1.3 85.9 - - + +
45A ARG* 1.3 59.8 + - - +
66A GLY 3.4 20.6 - - - +
67A LEU* 3.8 4.3 - - + +
69A PRO* 3.5 29.2 - - + +
70A VAL* 3.5 42.8 - - + -
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Residues in contact with ARG 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A LEU 3.3 5.6 - - - +
40A ALA* 3.8 18.0 - - + +
42A GLY 4.2 10.3 + - - -
43A GLU* 3.5 45.0 + - - +
44A TYR* 1.3 77.6 - - - +
46A GLY* 1.3 58.9 + - - +
66A GLY* 3.2 24.7 + - - -
67A LEU* 3.8 5.6 - - - -
144A GLU* 3.2 34.1 + - - +
145A ARG 5.8 2.5 - - - -
146A LEU* 3.8 15.7 - - + +
148A ASP* 5.1 3.9 - - - +
154A CYS* 4.1 15.1 - - - +
157A THR* 4.2 17.4 - - - +
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Residues in contact with GLY 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A SER* 3.3 5.7 - - - -
39A LEU 2.9 28.8 + - - -
45A ARG* 1.3 76.0 - - - +
47A VAL* 1.3 63.1 + - - -
64A SER* 3.1 13.7 - - - -
67A LEU* 3.5 10.8 - - - +
146A LEU* 3.5 15.1 - - - +
148A ASP* 5.1 5.4 - - - -
149A PHE* 5.3 0.2 - - - -
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Residues in contact with VAL 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ALA* 4.5 1.6 - - + -
37A ARG 3.3 14.8 - - - +
38A SER* 4.6 0.2 - - - -
46A GLY* 1.3 72.5 - - - +
48A VAL* 1.3 72.1 + - - +
49A THR* 4.2 11.3 + - - +
62A ASN* 3.8 2.3 + - - +
63A LEU* 3.6 3.1 - - - -
64A SER* 2.8 35.6 + - - +
67A LEU* 3.7 1.3 - - - +
146A LEU* 3.6 24.5 - - + -
149A PHE* 4.0 17.5 - - + -
152A TYR* 3.6 39.3 - - + +
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Residues in contact with VAL 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A TYR* 4.1 1.0 - - - +
36A ALA* 3.2 3.5 - - - +
37A ARG* 2.9 34.2 + - + +
39A LEU* 3.3 36.1 - - + -
47A VAL* 1.3 73.4 - - - +
49A THR* 1.3 64.1 + - - +
50A ALA 4.3 0.2 - - - -
61A ILE* 3.8 18.2 - - + -
62A ASN 3.4 2.9 - - - -
63A LEU* 3.6 20.4 - - + -
67A LEU* 3.4 19.3 - - + -
74A CYS* 5.0 1.6 - - + -
78A MET* 3.8 32.9 - - + +
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Residues in contact with THR 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A TYR* 4.2 17.5 - - + -
35A TYR 3.5 9.6 - - - +
36A ALA* 3.7 9.4 - - + +
47A VAL* 4.2 7.8 + - - +
48A VAL* 1.3 79.0 + - - +
50A ALA* 1.3 60.4 + - - +
51A ILE* 3.9 25.7 - - + +
60A HIS 3.5 1.0 - - - +
61A ILE* 3.3 6.1 - - - +
62A ASN* 2.8 57.0 + - + +
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Residues in contact with ALA 50 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A TRP* 5.9 0.2 - - + -
34A TYR* 3.3 5.7 - - - +
35A TYR* 2.7 35.7 + - + +
48A VAL 4.3 0.2 - - - -
49A THR* 1.3 71.3 - - - +
51A ILE* 1.3 62.7 + - - +
52A PRO* 3.7 4.4 - - - +
59A LEU* 3.9 7.4 - - + -
60A HIS 3.4 4.9 - - - -
61A ILE* 3.9 16.6 - - + -
78A MET* 4.2 6.7 - - - -
82A PHE* 3.7 32.3 - - + -
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Residues in contact with ILE 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A SER* 3.8 13.9 - - - +
34A TYR* 4.0 7.6 - - + -
49A THR* 3.9 21.5 - - + +
50A ALA* 1.3 77.4 - - - +
52A PRO* 1.3 72.6 - - - +
53A ASP 3.6 0.2 + - - -
59A LEU* 3.7 2.8 - - - +
60A HIS* 2.7 52.7 + - + +
62A ASN* 5.4 7.9 - - + -
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Residues in contact with PRO 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A TRP* 3.7 6.7 - - + -
12A TRP* 3.5 52.5 - - + +
16A LEU* 4.9 4.7 - - + -
32A ASP 5.8 0.2 - - - +
33A SER* 3.4 22.8 - - - +
34A TYR* 4.4 1.8 - - - -
50A ALA 3.7 7.2 - - - +
51A ILE* 1.3 91.0 - - - +
53A ASP* 1.3 59.7 + - - +
54A ILE* 3.6 13.3 + - + +
58A THR 3.9 2.5 - - - +
59A LEU* 3.8 11.2 - - + -
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Residues in contact with ASP 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A TRP* 3.5 1.9 - - - -
52A PRO* 1.3 71.8 - - - +
54A ILE* 1.3 58.6 + - - +
55A ALA* 3.8 6.2 + - - +
56A ARG* 3.4 28.7 + - - +
57A HIS* 2.9 24.4 + - - -
58A THR* 2.8 25.7 + - - +
60A HIS* 3.8 23.4 + - + +
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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