Contacts of the strand formed by residues 50 - 58 (chain A) in PDB entry 1M27
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 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A LEU* 3.4 3.3 - - - +
47A TYR 2.9 30.0 + - - +
48A HIS 3.8 13.5 - - - -
49A GLY* 1.3 81.4 - - - +
51A ILE* 1.3 64.8 + - - +
52A TYR* 3.6 27.8 - - + -
277B SER 4.5 5.2 - - - -
278B LEU* 3.4 37.9 - - + +
280B ILE* 3.9 25.4 - - + -
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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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16A GLY 5.6 0.4 - - - -
17A GLU* 3.9 33.9 - - + +
20A LEU* 3.7 17.9 - - + -
21A LEU* 4.2 11.7 - - + -
44A CYS* 3.6 32.8 - - + -
45A VAL 3.5 3.8 - - - +
46A LEU* 4.1 15.9 - - + -
49A GLY 4.6 0.2 - - - +
50A TYR* 1.3 78.4 - - - +
52A TYR* 1.3 61.2 + - - +
53A THR* 3.5 8.0 + - - +
278B LEU* 2.8 33.3 + - + +
279B THR* 3.3 13.0 - - - +
280B ILE 2.9 24.9 + - - -
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Residues in contact with TYR 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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43A LEU 3.3 2.4 - - - +
44A CYS* 3.3 3.5 - - - -
45A VAL* 2.8 41.2 + - + +
47A TYR* 3.4 47.5 + + + -
50A TYR* 3.6 30.5 - - + +
51A ILE* 1.3 72.1 - - - +
53A THR* 1.3 60.4 + - - +
54A TYR* 4.1 14.6 + - + -
95A VAL* 3.6 36.3 - - + -
280B ILE* 3.4 26.7 - - + +
282B ALA* 4.2 13.9 - - + -
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Residues in contact with THR 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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32A ARG* 4.4 2.1 + - - +
42A CYS* 3.5 38.6 - - + -
43A LEU 3.4 2.7 - - - -
44A CYS* 4.1 14.0 - - - -
51A ILE* 3.6 4.7 + - - +
52A TYR* 1.3 74.1 - - - +
54A TYR* 1.3 65.9 + - - +
55A ARG* 4.1 1.2 + - + +
300A FLC 4.3 2.5 - - - +
279B THR* 3.1 26.8 + - - +
280B ILE 2.9 12.2 + - - -
281B TYR* 3.6 21.3 - - + -
282B ALA 2.9 26.5 + - - +
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Residues in contact with TYR 54 (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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42A CYS* 3.4 2.9 - - - -
43A LEU* 2.8 57.9 + - + +
45A VAL* 4.4 14.1 - - + -
52A TYR* 4.1 20.4 - - + -
53A THR* 1.3 74.8 - - - +
55A ARG* 1.3 66.6 + - - +
56A VAL* 3.7 0.4 + - + -
66A ALA* 5.0 9.6 - - + -
67A GLU* 4.8 2.5 - - + +
94A ILE* 3.5 26.9 - - + +
95A VAL* 3.1 38.9 + - + +
282B ALA* 3.4 33.4 - - + +
283B GLN* 3.5 24.7 + - - -
284B VAL* 4.1 11.0 - - + -
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Residues in contact with ARG 55 (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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40A VAL* 4.4 20.0 - - + -
41A TYR 3.4 4.7 - - - +
42A CYS* 4.7 6.7 - - - -
53A THR* 4.1 1.0 + - + +
54A TYR* 1.3 74.0 - - - +
56A VAL* 1.3 59.8 + - - +
57A SER* 5.5 0.6 + - - -
65A SER 4.0 0.2 - - - +
66A ALA* 3.5 2.3 - - - -
67A GLU* 2.8 75.8 + - + +
300A FLC 2.9 37.3 + - - +
281B TYR* 3.4 45.7 - - + +
282B ALA 4.7 1.4 + - - -
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Residues in contact with VAL 56 (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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31A LEU* 4.9 4.7 - - + -
40A VAL* 3.7 2.1 - - - +
41A TYR* 2.7 50.7 + - + +
43A LEU* 4.4 17.5 - - + +
54A TYR* 4.1 9.0 - - + +
55A ARG* 1.3 79.3 - - - +
57A SER* 1.3 66.3 + - - +
64A TRP* 3.7 22.7 - - + -
65A SER 3.4 10.8 - - - +
66A ALA* 4.2 15.7 - - + -
80A ILE* 4.4 11.0 - - + -
83A LEU* 4.2 24.9 - - + -
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Residues in contact with SER 57 (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 GLY 4.0 14.1 - - - -
40A VAL* 4.4 13.9 - - - -
55A ARG 5.5 0.3 + - - -
56A VAL* 1.3 77.9 - - - +
58A GLN* 1.3 67.1 + - - +
59A THR* 5.3 0.7 - - - +
63A SER 3.7 0.7 - - - +
64A TRP* 3.6 11.3 - - - -
65A SER* 3.1 34.3 + - - +
74A LYS* 5.8 2.6 + - - -
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Residues in contact with GLN 58 (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 MET* 3.7 19.6 - - - +
39A GLY 4.5 4.7 + - - +
41A TYR* 5.7 0.5 - - - -
57A SER* 1.3 80.4 + - - +
59A THR* 1.3 71.0 + - - +
62A GLY* 3.2 30.2 + - - -
63A SER 3.2 7.0 - - - +
64A TRP* 3.4 41.5 - - + +
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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