Contacts of the strand formed by residues 37 - 41 (chain J) in PDB entry 1S5E
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 MET 37 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29J GLU* 3.6 3.3 - - - +
30J SER* 3.0 33.3 + - - +
35J ARG* 3.1 36.6 + - - +
36J GLU* 1.3 75.0 - - - +
38J ALA* 1.3 61.7 + - - +
39J ILE* 3.7 33.2 - - + -
49J GLN* 3.5 31.9 - - + +
50J VAL 3.5 13.2 - - - +
51J GLU 5.0 0.2 - - - -
52J VAL* 3.9 13.9 - - + -
69J LYS* 4.7 9.0 - - - -
1N THR* 3.7 19.3 - - + -
2N PRO* 4.3 7.2 - - - +
8N LEU* 4.5 4.3 - - + -
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Residues in contact with ALA 38 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27J TYR* 4.2 22.4 - - + +
28J THR 3.1 11.2 - - - +
29J GLU* 4.8 1.8 - - + -
37J MET* 1.3 75.4 - - - +
39J ILE* 1.3 67.1 + - - +
49J GLN* 3.2 5.4 - - - +
50J VAL* 2.9 38.1 + - + +
69J LYS* 4.0 24.2 - - + +
72J LEU* 5.2 3.6 - - + -
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Residues in contact with ILE 39 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26J SER* 3.9 1.0 + - - +
27J TYR* 3.7 0.3 - - - -
28J THR* 2.8 53.4 + - + +
37J MET* 3.7 24.2 - - + -
38J ALA* 1.3 81.0 - - - +
40J ILE* 1.3 71.2 + - - +
41J THR* 4.8 3.4 - - + -
47J THR* 3.8 15.0 - - + -
48J PHE 3.2 12.6 - - - +
49J GLN* 4.7 2.5 - - + -
93J PRO* 5.2 1.3 - - + -
2N PRO 3.6 23.1 - - - +
3N GLN* 3.6 17.7 - - - +
4N ASN* 4.0 19.5 - - - +
8N LEU* 5.0 6.5 - - + -
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Residues in contact with ILE 40 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24J ILE* 3.9 16.8 - - + -
26J SER* 3.2 12.3 - - - +
27J TYR* 3.9 22.0 - - + -
38J ALA 5.8 0.4 - - - -
39J ILE* 1.3 79.1 - - - +
41J THR* 1.3 65.0 + - - +
42J PHE* 3.8 27.8 - - + -
46J ALA 4.0 0.2 - - - +
47J THR* 3.4 4.2 - - - +
48J PHE* 2.9 46.8 + - + +
72J LEU* 4.1 29.2 - - + -
82J VAL* 5.9 0.4 - - + -
85J LEU* 4.5 5.8 - - + -
96J ILE* 3.9 22.0 - - + -
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Residues in contact with THR 41 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24J ILE* 3.7 5.4 - - - +
25J PHE* 2.7 41.2 + - - -
26J SER* 2.6 35.8 + - - +
39J ILE* 4.8 4.7 - - + -
40J ILE* 1.3 78.4 - - - +
42J PHE* 1.3 65.3 + - - +
45J GLY* 5.0 2.5 - - - -
46J ALA 3.2 9.2 - - - -
47J THR* 3.5 26.0 - - + +
3N GLN 5.0 3.6 - - - +
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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