Contacts of the strand formed by residues 23 - 27 (chain K) in PDB entry 4M75
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 THR 23 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22K LYS* 1.3 73.6 - - - +
24K VAL* 1.3 59.3 + - - +
35K SER* 5.6 2.5 - - - +
36K GLY* 3.6 8.1 - - - +
37K ARG* 3.7 51.7 + - + +
83K GLU* 3.7 1.2 - - - -
84K GLN* 3.2 46.4 + - - +
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Residues in contact with VAL 24 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19K ILE* 3.9 31.9 - - + -
22K LYS 3.7 7.9 - - - +
23K THR* 1.3 79.4 - - - +
25K ASN* 1.3 66.3 + - - +
26K VAL* 4.2 3.5 + - + -
34K TYR 4.1 0.9 - - - +
35K SER* 3.8 2.8 + - - -
36K GLY 3.0 37.8 + - - +
38K LEU* 3.4 30.1 - - + -
49K LEU* 3.8 10.2 - - + +
81K ILE* 4.0 18.6 - - + -
82K SER 3.2 10.3 - - - +
83K GLU* 4.0 2.5 - - - -
84K GLN* 4.5 3.1 - - - +
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Residues in contact with ASN 25 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24K VAL* 1.3 74.0 - - - +
26K VAL* 1.3 61.9 + - - +
27K LYS 4.1 0.7 - - - -
33K LEU* 3.5 26.8 - - + +
34K TYR 4.2 0.4 - - - -
35K SER* 3.3 26.7 - - - -
80K TYR* 3.4 10.1 - - + +
81K ILE* 3.1 6.9 - - - +
82K SER* 2.6 48.0 + - - +
84K GLN* 3.7 27.5 + - - +
65L MSE 4.9 3.0 - - - -
67L HIS* 4.2 19.3 + - + -
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Residues in contact with VAL 26 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24K VAL* 4.8 2.7 - - + -
25K ASN* 1.3 77.1 - - - +
27K LYS* 1.3 61.8 + - - +
28K LEU* 3.9 1.7 + - + -
32K LEU 3.9 0.9 - - - +
33K LEU* 4.2 3.1 - - - +
34K TYR* 3.4 31.4 + - - +
47K VAL* 3.9 25.6 - - + -
49K LEU* 4.4 16.8 - - + -
73K LEU* 3.4 28.0 - - + +
78K VAL* 3.6 29.8 - - + -
80K TYR 3.3 4.9 - - - +
81K ILE* 4.2 17.3 - - + -
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Residues in contact with LYS 27 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25K ASN 4.1 1.0 - - - -
26K VAL* 1.3 74.8 - - - +
28K LEU* 1.3 72.9 + - - +
31K GLY* 3.2 29.4 - - - -
32K LEU 4.0 3.1 - - - +
33K LEU* 4.4 11.8 - - + +
56K TYR 4.0 0.6 + - - -
57K GLU 2.5 31.9 + - - -
78K VAL* 3.1 8.0 - - - +
79K MSE 2.8 31.9 + - + -
80K TYR* 3.1 45.2 + - + +
28L ARG* 3.9 13.5 - - - +
50L GLU* 3.0 30.3 + - - +
64L VAL* 4.2 3.4 - - - +
65L MSE 5.4 0.6 - - - -
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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