Contacts of the strand formed by residues 21 - 26 (chain A) in PDB entry 1M1B
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 GLU 21 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A MET* 3.1 50.8 - - + +
17A SER* 2.6 24.4 + - - +
19A ASP* 3.5 11.1 - - - +
20A LEU* 1.3 77.3 - - - +
22A PHE* 1.3 71.3 + - - +
41A LYS* 3.1 37.8 + - - +
233A SER 2.8 14.5 + - - +
234A MET* 3.3 8.9 - - + -
235A VAL 2.9 26.5 + - - -
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Residues in contact with PHE 22 (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 MET* 4.0 5.2 - - - +
20A LEU* 3.2 43.7 - - + -
21A GLU* 1.3 82.6 + - - +
23A ILE* 1.3 66.8 + - - +
40A PHE* 3.7 30.9 - + + -
41A LYS* 4.3 2.9 + - - +
42A GLY 3.9 8.3 + - - -
224A THR* 4.0 17.0 - - + -
228A ARG* 4.3 11.7 - - - -
235A VAL* 3.6 20.6 - - + -
237A TRP* 3.8 29.2 - + - +
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Residues in contact with ILE 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 4.8 5.6 - - + -
14A MET* 4.0 5.4 - - + -
22A PHE* 1.3 77.1 - - - +
24A MET* 1.3 60.3 + - - +
40A PHE* 4.7 0.2 - - - -
42A GLY* 3.4 32.5 - - - -
43A ILE 3.9 4.9 - - - +
44A TRP* 4.2 12.7 - - + +
83A LEU* 4.0 22.0 - - + -
234A MET* 3.7 34.3 - - + +
235A VAL 3.2 5.3 + - - +
236A ILE* 3.4 36.7 - - + -
237A TRP* 3.2 28.1 + - - +
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Residues in contact with MET 24 (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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23A ILE* 1.3 74.4 - - - +
25A GLU* 1.3 84.1 + - + +
26A ALA 3.6 0.3 + - - -
35A VAL* 3.7 13.0 - - + +
40A PHE* 3.6 37.2 - - + -
42A GLY 3.1 6.9 + - - -
43A ILE* 3.3 9.5 - - - +
44A TRP* 2.8 20.7 + - - -
237A TRP* 3.4 38.1 - - + +
240A HIS* 4.0 23.8 - - + +
241A ASN* 3.7 25.6 - - - +
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Residues in contact with GLU 25 (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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24A MET* 1.3 77.2 - - + +
26A ALA* 1.3 71.6 + - - +
27A HIS* 3.0 16.7 + - - -
35A VAL* 3.7 1.0 - - - +
44A TRP* 3.1 17.7 - - + +
46A SER* 4.4 1.6 - - - -
49A SER* 3.5 11.2 + - - -
237A TRP 2.9 14.8 + - - +
238A ALA 3.2 17.3 - - - +
239A ASN* 3.0 26.2 - - - +
240A HIS 3.6 5.8 - - - +
241A ASN* 2.8 40.5 + - - +
242A LEU* 2.5 36.8 + - - +
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Residues in contact with ALA 26 (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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24A MET 3.6 0.2 + - - -
25A GLU* 1.3 82.9 - - - +
27A HIS* 1.3 59.8 + - - +
28A ASN 3.7 0.4 - - - +
31A SER* 3.6 19.7 - - - +
32A ALA* 3.7 21.5 - - - +
35A VAL* 4.1 3.8 - - + -
43A ILE* 3.7 22.7 - - + -
44A TRP 3.1 14.4 + - - +
45A GLY* 3.8 11.3 - - - -
46A SER 4.0 3.1 + - - -
74A MET* 3.9 8.6 - - + +
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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