Contacts of the strand formed by residues 32 - 41 (chain A) in PDB entry 1MRA
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 ALA 32 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A ASN* 3.3 3.7 - - - +
16A VAL* 2.5 54.3 + - + +
18A LEU* 3.7 20.0 - - + -
29A VAL* 5.7 0.4 - - + -
31A THR* 1.3 75.7 - - - +
33A PRO* 1.3 67.6 - - + +
34A LEU* 3.4 9.7 + - + +
52A PHE* 4.5 11.7 - - + -
321A LEU* 4.4 6.7 - - + +
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Residues in contact with PRO 33 (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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14A VAL 3.7 2.7 - - - +
15A ASN* 3.3 17.0 - - - +
29A VAL* 5.2 1.3 - - + -
31A THR* 4.1 5.4 - - - +
32A ALA* 1.3 83.5 - - - +
34A LEU* 1.3 58.9 + - - +
52A PHE* 3.5 19.9 - - + -
53A ALA* 2.8 38.0 + - + +
54A TYR 4.1 5.2 - - - +
55A THR* 3.7 32.5 - - - +
56A PRO* 3.8 10.3 - - + -
59A LEU* 4.0 18.2 - - + -
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Residues in contact with LEU 34 (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 ALA* 3.3 3.8 - - - -
14A VAL* 2.9 37.0 + - + +
16A VAL* 4.0 23.6 - - + -
32A ALA* 3.4 11.2 + - + +
33A PRO* 1.3 83.1 - - - +
35A VAL* 1.3 66.3 + - - +
36A LEU* 4.0 21.5 - - + -
50A TYR* 4.4 8.3 - - + -
51A LEU 3.0 18.6 - - - +
52A PHE* 3.8 21.3 - - + -
53A ALA 4.8 0.4 - - - +
59A LEU* 3.5 2.8 - - - +
321A LEU* 4.3 13.2 - - + +
322A ALA* 4.1 25.8 - - + -
325A VAL* 5.0 1.6 - - + -
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Residues in contact with VAL 35 (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 THR* 4.1 18.2 - - - -
12A ARG 3.3 8.1 - - - +
13A ALA* 4.5 2.0 - - + -
34A LEU* 1.3 73.6 - - - +
36A LEU* 1.3 64.6 + - - +
37A ILE* 3.8 5.7 + - + +
50A TYR* 3.2 3.3 - - - -
51A LEU* 2.7 42.5 + - + +
53A ALA* 5.6 1.6 - - + -
59A LEU* 3.4 27.1 - - + +
62A LEU* 4.7 12.8 - - + -
63A LYS* 4.4 25.1 - - + +
66A LEU* 4.0 24.0 - - + -
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Residues in contact with LEU 36 (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 ARG 3.6 0.9 - - - +
11A THR* 3.3 6.6 - - - -
12A ARG* 2.6 53.6 + - + +
14A VAL* 3.7 29.4 - - + -
34A LEU* 4.0 16.2 - - + -
35A VAL* 1.3 76.1 - - - +
37A ILE* 1.3 61.5 - - - +
38A ASP* 5.1 1.6 - - - +
49A SER 3.8 3.8 - - - -
50A TYR* 4.0 10.8 - - + -
322A ALA* 6.4 0.2 - - + -
325A VAL* 4.5 8.1 - - + -
349A TRP* 3.5 26.2 - - + -
354A ILE* 3.7 42.4 - - + -
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Residues in contact with ILE 37 (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 LEU* 3.9 23.6 - - + -
10A ARG 3.5 2.2 - - - -
11A THR* 4.1 16.8 - - + -
35A VAL* 4.2 8.1 - - + +
36A LEU* 1.3 77.3 - - - +
38A ASP* 1.3 66.9 - - - +
48A HIS* 3.2 8.0 - - - -
49A SER* 2.9 50.7 + - - +
51A LEU* 3.9 30.7 - - + -
66A LEU* 4.1 13.9 - - + -
106A GLY* 4.0 15.3 - - - +
107A ILE* 5.2 1.1 - - - -
110A ALA* 4.0 15.9 - - + -
349A TRP* 3.7 4.4 - - - -
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Residues in contact with ASP 38 (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 GLY 4.4 0.2 - - - -
9A LEU* 3.4 5.2 - - - +
10A ARG* 2.8 67.3 + - + +
12A ARG* 3.1 26.3 + - - -
36A LEU 5.1 1.0 - - - +
37A ILE* 1.3 74.1 - - - +
39A LEU* 1.3 60.8 + - - +
40A ALA 3.9 1.3 + - - -
46A VAL* 3.8 11.7 - - + +
47A GLY 3.3 2.2 - - - -
48A HIS* 2.7 19.4 + - - -
349A TRP* 2.7 27.8 + - - -
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Residues in contact with LEU 39 (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 ILE* 3.9 35.9 - - + -
8A GLY 3.5 3.6 - - - +
9A LEU* 3.8 14.8 - - + -
37A ILE 4.1 0.2 - - - -
38A ASP* 1.3 72.7 - - - +
40A ALA* 1.3 60.9 + - - +
41A THR* 3.7 6.8 - - + +
46A VAL* 3.6 3.2 - - - +
47A GLY* 2.9 35.1 + - - +
73A ILE* 3.7 30.1 - - + -
78A LEU* 4.2 7.2 - - + -
107A ILE* 4.5 9.0 - - + +
110A ALA* 3.9 17.9 - - + +
111A ALA* 3.8 32.3 - - + +
114A ALA* 4.9 2.2 - - + -
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Residues in contact with ALA 40 (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 ILE* 3.5 7.1 - - - +
7A THR* 2.6 43.5 + - - +
8A GLY* 2.9 20.3 + - - +
38A ASP 3.9 2.0 + - - -
39A LEU* 1.3 69.0 - - - +
41A THR* 1.3 63.4 + - - +
45A VAL 4.2 3.1 - - - -
46A VAL* 4.6 12.8 - - + +
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Residues in contact with THR 41 (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 VAL* 4.1 9.1 - - - +
5A LEU 3.2 11.0 - - - +
6A ILE* 5.2 0.7 - - - -
7A THR* 3.0 8.8 + - - +
39A LEU* 3.7 11.4 - - + +
40A ALA* 1.3 79.6 - - - +
42A SER* 1.3 63.5 + - - +
43A ALA* 2.9 15.3 + - - +
44A GLY* 3.1 11.6 + - - -
45A VAL* 3.0 37.1 + - + +
78A LEU* 4.7 14.1 - - + -
114A ALA* 4.1 18.8 - - + -
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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