Contacts of the strand formed by residues 2 - 14 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B VAL* 1.3 76.6 + - - +
3B PHE* 1.3 61.0 + - - +
4B HIS* 3.9 21.2 + - + +
45B LYS 3.4 1.0 - - - +
46B LEU* 3.3 7.1 - - - -
47B GLY 2.8 35.2 + - - +
48B GLN* 4.2 3.6 - - - +
49B GLU* 4.7 1.2 + - - +
59B TYR* 2.7 40.7 + - - +
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Residues in contact with PHE 3 (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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1A VAL* 3.5 42.6 - - + -
46A LEU* 3.9 40.4 - - + -
47A GLY 4.6 4.3 - - - -
48A GLN* 4.1 16.9 + - + +
60A PHE* 4.3 11.9 - + - -
62A THR* 5.1 0.2 - - + -
1B VAL 3.8 1.6 + - - -
2B ASP* 1.3 71.6 - - - +
4B HIS* 1.3 77.0 + - - +
44B LEU* 4.5 18.2 - - + -
45B LYS 3.4 11.9 - - - -
46B LEU* 3.9 13.7 - - + -
427B TRP* 3.2 53.4 - + - +
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Residues in contact with HIS 4 (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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2B ASP* 3.9 28.3 - - + +
3B PHE* 1.3 80.6 + - - +
5B GLY* 1.3 60.2 + - - +
45B LYS* 2.7 50.6 + - + +
47B GLY 6.0 0.4 - - - -
59B TYR* 4.8 5.6 + - - -
61B ASP* 6.1 1.1 - - - -
427B TRP* 2.7 47.8 + - - +
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Residues in contact with GLY 5 (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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4B HIS* 1.3 79.6 - - - +
6B TYR* 1.3 61.5 + - - +
43B GLU* 3.1 16.4 - - - -
45B LYS* 4.4 11.1 - - - +
426B TRP* 3.3 6.4 - - - +
427B TRP* 3.0 35.9 + - - +
3E GLC 5.0 3.7 + - - -
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Residues in contact with TYR 6 (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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5B GLY* 1.3 75.4 - - - +
7B ALA* 1.3 88.4 + - - +
8B ARG* 3.0 42.3 + - + +
33B ARG* 3.4 3.1 + - - -
41B TYR* 3.8 19.5 - + - -
42B ALA* 3.2 0.7 - - - +
43B GLU* 2.7 38.6 + - + +
424B GLU* 2.6 40.6 + - + -
425B ILE 3.3 16.2 - - - -
426B TRP* 3.9 16.2 - + + -
427B TRP* 3.3 4.4 - - - -
2E GLC 3.7 36.1 - - - -
3E GLC 3.8 16.8 - - - +
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Residues in contact with ALA 7 (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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60A PHE* 4.1 15.0 - - + -
84A ALA* 5.2 3.8 - - + -
6B TYR* 1.3 82.2 - - - +
8B ARG* 1.3 62.0 + - - +
41B TYR 3.1 10.8 - - - +
42B ALA* 3.8 12.6 - - + -
423B MET* 4.2 7.0 - - + -
424B GLU* 3.5 3.8 - - - +
425B ILE* 2.9 47.0 + - + +
427B TRP* 4.1 7.0 - - + -
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Residues in contact with ARG 8 (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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84A ALA* 5.6 0.2 - - - +
6B TYR* 3.0 35.1 + - + +
7B ALA* 1.3 75.5 - - - +
9B SER* 1.3 63.5 + - - +
33B ARG* 3.7 6.2 - - - +
37B GLU* 3.7 29.3 + - - +
39B GLU* 2.9 41.2 + - - +
40B THR* 3.2 4.7 - - - +
41B TYR* 2.9 51.8 + - - +
116B ASP* 4.3 4.2 + - - -
422B GLN* 3.9 10.8 - - - +
423B MET* 3.3 15.0 - - - +
424B GLU* 4.5 3.6 - - + -
1E BGC 4.0 7.9 + - - -
2E GLC 3.0 28.3 + - - -
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Residues in contact with SER 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ALA* 3.4 21.7 + - - -
103A GLY* 3.7 6.2 + - - -
104A LYS* 3.2 24.9 + - - +
8B ARG* 1.3 76.9 - - - +
10B GLY* 1.3 58.6 + - - +
39B GLU 4.7 0.9 - - - -
40B THR* 2.7 26.6 + - - +
70B GLN* 3.7 2.6 + - - -
422B GLN* 3.9 5.5 - - - +
423B MET* 2.9 38.9 + - - +
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Residues in contact with GLY 10 (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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103A GLY* 4.6 8.5 - - - -
125A PRO* 3.9 14.2 - - - +
126A GLY 4.9 3.4 - - - -
9B SER* 1.3 77.1 + - - +
11B ILE* 1.3 61.3 + - - +
20B GLN* 5.9 0.2 - - - -
70B GLN* 3.1 31.5 + - - +
421B ALA 3.2 14.6 - - - -
422B GLN* 3.9 6.5 - - - +
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Residues in contact with ILE 11 (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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125A PRO* 4.0 7.4 - - + +
126A GLY* 3.9 26.9 - - - +
127A ALA* 4.1 12.3 - - + +
143A ALA* 3.9 19.3 - - + +
144A THR 3.9 20.4 - - - +
145A ARG* 4.0 23.6 - - + +
170A ASP* 5.1 0.2 - - - +
10B GLY* 1.3 74.2 - - - +
12B GLY* 1.3 60.6 + - - +
13B TRP* 3.8 35.2 - - + -
20B GLN* 4.4 3.9 - - - +
70B GLN* 5.0 1.6 - - - +
376B PHE* 5.0 0.7 - - - -
420B GLY* 3.4 1.2 - - - -
421B ALA* 3.0 36.8 + - + +
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Residues in contact with GLY 12 (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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145A ARG* 3.0 29.3 + - - +
11B ILE* 1.3 77.2 - - - +
13B TRP* 1.3 65.9 + - - -
19B GLU* 3.8 0.2 - - - -
20B GLN* 3.2 32.3 + - - +
70B GLN* 5.6 1.2 - - - +
419B PHE 3.4 10.1 - - - -
420B GLY* 4.0 0.9 - - - -
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Residues in contact with TRP 13 (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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143A ALA* 4.3 19.3 - - + -
144A THR 5.9 0.4 - - - -
145A ARG* 2.9 18.5 - - - +
170A ASP* 2.8 32.2 + - + -
172A PHE* 4.7 10.2 - + - -
195A ARG* 4.8 4.5 - - - +
197A ASN* 3.6 14.6 - - - -
11B ILE* 3.8 38.6 - - + -
12B GLY* 1.3 74.8 - - - -
14B THR* 1.3 63.3 + - - +
18B GLY 3.6 4.7 - - - +
20B GLN* 3.7 4.8 - - - +
418B THR* 3.1 7.6 - - - -
419B PHE* 2.8 78.1 + + + -
420B GLY* 4.0 15.3 - - - -
421B ALA* 5.0 0.9 - - + -
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Residues in contact with THR 14 (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 TRP* 1.3 76.0 - - - +
15B GLY* 1.3 68.5 + - - +
16B SER* 3.5 10.3 - - - +
17B GLY* 2.9 27.7 + - - +
18B GLY 3.1 6.7 + - - +
19B GLU 2.6 22.6 + - - -
21B GLN* 3.2 33.5 + - - +
416B GLU* 3.4 36.3 - - + +
417B TRP 3.7 2.7 - - - +
418B THR* 3.8 2.8 - - + +
419B PHE* 4.6 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