Contacts of the strand formed by residues 41 - 45 (chain K) in PDB entry 1BTH
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 LEU 41 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32K MET* 4.1 24.5 - - + -
33K LEU 3.5 3.6 - - - +
34K PHE* 6.0 2.5 - - + -
40K LEU* 1.3 76.1 - - - +
42K CYS* 1.3 86.8 + - - +
73K ARG* 4.9 4.9 - - + +
141K TRP* 3.6 38.1 - - + +
142K GLY* 4.6 0.4 - - - -
151K GLN* 3.8 21.3 - - - +
193K GLY* 3.9 16.1 - - - +
17Q ARG* 3.1 44.6 + - + +
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Residues in contact with CYS 42 (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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32K MET* 3.8 3.8 - - - -
33K LEU* 3.0 36.9 + - + +
40K LEU* 4.4 6.3 - - + -
41K LEU* 1.3 88.3 - - - +
43K GLY* 1.3 62.9 + - - +
58K CYS* 2.0 53.6 - - + -
141K TRP* 5.4 1.5 - - - -
193K GLY 3.6 13.0 - - - -
195K SER* 3.7 3.6 - - - -
16Q ALA* 3.7 18.4 - - - -
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Residues in contact with GLY 43 (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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30K GLN* 3.9 12.3 - - - -
31K VAL 3.5 10.1 - - - -
33K LEU* 3.9 1.6 - - - +
42K CYS* 1.3 78.0 - - - +
44K ALA* 1.3 60.1 + - - +
54K THR* 2.8 19.6 + - - -
141K TRP* 5.5 2.5 - - - -
193K GLY 3.9 3.1 + - - -
194K ASP* 4.6 1.8 - - - -
195K SER 2.7 14.1 + - - +
196K GLY 3.3 12.0 - - - -
197K GLY* 3.9 4.9 - - - -
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Residues in contact with ALA 44 (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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29K TRP 3.7 1.2 - - - +
30K GLN* 4.0 6.8 + - - -
31K VAL* 3.1 30.0 + - + +
33K LEU* 3.7 16.8 - - + -
43K GLY* 1.3 75.6 - - - +
45K SER* 1.3 61.5 + - - +
52K VAL* 3.5 24.5 - - + -
53K LEU 3.2 10.1 - - - +
54K THR* 3.7 8.5 - - - -
196K GLY 3.5 8.5 + - - -
197K GLY* 4.1 0.4 - - - -
198K PRO* 4.1 5.0 - - - +
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Residues in contact with SER 45 (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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29K TRP* 3.1 14.1 + - - +
31K VAL* 4.2 5.4 - - - -
44K ALA* 1.3 78.1 - - - +
46K LEU* 1.3 61.5 + - - +
47K ILE* 3.6 0.6 + - - -
52K VAL* 3.1 4.5 - - - -
53K LEU* 2.7 45.9 + - - +
121K VAL* 3.4 14.4 - - - +
198K PRO* 3.3 18.0 - - - +
209K GLN* 3.2 30.3 + - - -
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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