Contacts of the strand formed by residues 2 - 14 (chain A) in PDB entry 2MPR
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 ASP 2 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A VAL* 1.3 77.5 + - - +
3A PHE* 1.3 61.0 + - - +
4A HIS* 3.9 20.9 + - + +
45A LYS 3.5 0.9 - - - +
46A LEU* 3.3 7.1 - - - -
47A GLY 2.8 35.1 + - - +
48A GLN* 4.2 4.3 - - - -
49A GLU 4.6 1.3 + - - -
59A TYR* 2.7 40.6 + - - +
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Residues in contact with PHE 3 (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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1A VAL 3.8 2.2 + - - +
2A ASP* 1.3 72.5 - - - +
4A HIS* 1.3 77.8 + - - +
44A LEU* 4.5 17.0 - - + -
45A LYS 3.4 12.6 - - - -
46A LEU* 3.8 14.1 - - + -
427A TRP* 3.2 54.3 - + - +
1C VAL* 3.6 39.7 - - + -
46C LEU* 3.9 39.3 - - + -
47C GLY 4.6 4.7 - - - -
48C GLN* 4.1 17.7 + - + +
60C PHE* 4.3 12.6 - + - -
62C THR* 5.1 0.9 - - + -
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Residues in contact with HIS 4 (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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2A ASP* 3.9 27.8 + - + +
3A PHE* 1.3 79.1 + - - +
5A GLY* 1.3 56.0 + - - +
45A LYS* 2.7 55.9 + - + +
47A GLY 6.1 0.4 - - - -
59A TYR* 4.9 5.8 + - - -
61A ASP* 6.1 0.9 - - - -
427A TRP* 2.7 47.9 + - - +
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Residues in contact with GLY 5 (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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4A HIS* 1.3 79.5 - - - +
6A TYR* 1.3 63.6 + - - +
43A GLU* 3.1 14.8 - - - -
45A LYS* 4.4 11.6 - - - +
426A TRP* 3.3 7.4 - - - +
427A TRP* 3.1 34.1 + - - +
3D GLC 4.9 3.4 + - - -
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Residues in contact with TYR 6 (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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5A GLY* 1.3 75.4 - - - +
7A ALA* 1.3 76.8 + - - +
8A ARG* 2.9 42.5 + - + +
33A ARG* 3.5 2.4 + - - -
41A TYR* 3.8 20.0 - + - -
42A ALA* 3.2 0.5 - - - +
43A GLU* 2.7 37.8 + - + +
424A GLU* 2.5 41.4 + - + -
425A ILE 3.3 15.5 - - - -
426A TRP* 3.9 16.8 - + + -
427A TRP* 3.4 4.7 - - - -
2D GLC 3.7 37.0 - - - -
3D GLC 3.8 16.6 - - - +
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Residues in contact with ALA 7 (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 TYR* 1.3 81.2 - - - +
8A ARG* 1.3 61.1 + - - +
41A TYR 3.1 11.2 - - - +
42A ALA* 3.8 12.3 - - + -
423A MET* 4.2 8.7 - - + -
424A GLU* 3.4 4.0 - - - +
425A ILE* 2.9 47.8 + - + +
427A TRP* 3.9 0.4 - - + -
60C PHE* 4.1 20.4 - - + -
84C ALA* 5.1 3.8 - - + -
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Residues in contact with ARG 8 (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 TYR* 2.9 37.5 + - - +
7A ALA* 1.3 75.1 - - - +
9A SER* 1.3 63.8 + - - +
33A ARG* 3.7 6.3 - - - +
37A GLU* 3.7 27.6 + - - +
39A GLU* 2.9 39.8 + - - +
40A THR* 3.2 5.1 - - - +
41A TYR* 2.9 52.8 + - - +
116A ASP* 4.4 4.2 + - - -
422A GLN* 3.9 10.8 - - - +
423A MET* 3.3 14.4 - - - +
424A GLU* 4.5 3.8 - - + +
1D BGC 4.0 7.7 + - - -
2D GLC 3.0 27.3 + - - -
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Residues in contact with SER 9 (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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8A ARG* 1.3 75.6 - - - +
10A GLY* 1.3 60.6 + - - +
39A GLU 4.6 1.1 - - - -
40A THR* 2.8 27.3 + - - +
70A GLN* 3.7 3.1 + - - -
422A GLN* 3.4 5.4 - - - +
423A MET* 2.8 39.6 + - - +
84C ALA* 3.4 20.8 + - - -
103C GLY* 3.5 6.4 + - - -
104C LYS* 3.2 24.9 + - - +
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Residues in contact with GLY 10 (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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9A SER* 1.3 78.2 + - - +
11A ILE* 1.3 62.0 + - - +
20A GLN* 5.9 0.2 - - - -
39A GLU 5.3 0.2 + - - -
70A GLN* 3.2 29.9 + - - +
421A ALA 3.2 13.2 - - - -
422A GLN* 3.9 6.7 - - - +
103C GLY* 4.6 8.9 - - - -
125C PRO* 3.9 14.7 - - - +
126C GLY 4.8 3.8 - - - -
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Residues in contact with ILE 11 (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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10A GLY* 1.3 75.7 - - - +
12A GLY* 1.3 62.3 + - - +
13A TRP* 3.8 36.3 - - + -
20A GLN* 4.5 4.1 - - - +
70A GLN* 5.0 2.0 - - - +
376A PHE* 4.9 1.0 - - - -
420A GLY* 3.3 1.4 - - - -
421A ALA* 2.9 36.8 + - + +
125C PRO* 4.0 15.0 - - + +
126C GLY* 3.9 25.4 - - - +
127C ALA* 4.0 12.1 - - + +
143C ALA* 3.9 18.2 - - + +
144C THR 4.0 13.7 - - - +
145C ARG* 4.1 22.4 - - + +
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Residues in contact with GLY 12 (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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11A ILE* 1.3 78.6 - - - +
13A TRP* 1.3 67.5 + - - -
19A GLU* 3.7 0.2 - - - -
20A GLN* 3.1 32.1 + - - +
70A GLN* 5.6 1.0 - - - +
419A PHE 3.3 10.5 - - - -
420A GLY* 4.0 0.7 - - - -
145C ARG* 3.0 28.7 + - - +
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Residues in contact with TRP 13 (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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11A ILE* 3.8 39.5 - - + -
12A GLY* 1.3 73.7 - - - -
14A THR* 1.3 62.9 + - - +
18A GLY 3.6 4.3 - - - +
20A GLN* 3.8 5.1 - - - +
418A THR* 3.1 7.1 - - - -
419A PHE* 2.8 76.3 + + + -
420A GLY* 4.1 15.5 - - - -
421A ALA* 4.9 0.9 - - + -
143C ALA* 4.3 20.0 - - + -
144C THR 5.9 0.2 - - - -
145C ARG* 3.0 17.4 - - - +
170C ASP* 2.7 30.8 + - + -
172C PHE* 4.7 13.3 - + - -
197C ASN* 3.6 14.4 - - - -
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Residues in contact with THR 14 (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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13A TRP* 1.3 74.6 - - - +
15A GLY* 1.3 66.5 + - - +
16A SER* 3.7 9.9 - - - +
17A GLY* 2.8 31.9 + - - +
18A GLY 3.0 6.9 + - - +
19A GLU 2.5 20.4 + - - -
21A GLN* 3.2 32.8 + - - +
416A GLU* 3.3 39.7 - - + +
417A TRP 3.7 3.1 - - - +
418A THR* 3.8 3.5 - - + +
419A PHE* 4.6 2.0 - - - -
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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