Contacts of the strand formed by residues 30 - 34 (chain K) in PDB entry 2BDI
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 GLN 30 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27K GLN* 3.0 18.0 + - - +
28K PRO 4.3 2.9 - - - +
29K TRP* 1.3 81.9 - - - +
31K ALA* 1.3 61.0 + - - +
43K SER* 3.6 18.3 + - - -
44K GLY 3.9 2.2 - - - -
66K GLY 4.1 4.2 - - - +
67K LEU* 3.9 13.4 - - - +
69K GLY 4.4 3.8 + - - -
70K LEU 5.3 3.9 + - - +
139K SER* 2.8 41.8 + - - +
140K GLY* 3.7 0.3 - - - -
141K TRP* 3.6 26.8 - - + -
155K LEU* 3.5 23.8 - - + +
198K PRO* 3.0 26.6 - - - +
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Residues in contact with ALA 31 (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 4.3 2.0 - - - +
30K GLN* 1.3 73.4 - - - +
32K ALA* 1.3 61.0 + - - +
33K LEU* 4.5 0.9 - - + -
43K SER* 3.0 10.7 - - - -
44K GLY* 2.7 52.7 + - - +
45K VAL* 4.3 0.7 - - - +
46K LEU 4.8 0.2 - - - +
52K VAL* 4.2 11.4 - - + -
65K ILE* 4.0 20.9 - - + -
66K GLY 3.7 4.0 - - - -
67K LEU* 4.0 9.4 - - + -
141K TRP* 4.5 2.9 - - - -
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Residues in contact with ALA 32 (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 4.3 0.2 - - - -
31K ALA* 1.3 71.2 - - - +
33K LEU* 1.3 64.7 + - - +
34K VAL* 4.0 5.6 - - + +
40K LEU* 3.8 11.9 - - + -
42K CYS 4.0 2.7 - - - -
64K THR 3.7 0.9 - - - +
65K ILE* 3.2 7.8 - - - -
66K GLY 2.8 39.1 + - - +
70K LEU* 4.2 12.8 - - + -
73K LEU* 4.8 4.9 - - + -
141K TRP* 3.6 29.1 - - + -
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Residues in contact with LEU 33 (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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31K ALA* 3.9 13.9 - - + +
32K ALA* 1.3 81.3 - - - +
34K VAL* 1.3 59.9 + - - +
40K LEU* 3.2 4.0 - - - +
41K PHE* 3.0 46.7 + - + -
42K CYS* 2.5 39.7 + - + +
43K SER 3.9 12.8 - - - +
44K GLY* 4.0 3.6 - - - +
52K VAL* 5.0 3.4 - - + -
54K SER* 4.2 8.7 - - - +
58K CYS* 4.7 4.5 - - + -
63K TYR* 4.4 9.2 - - + -
64K THR 4.2 3.6 - - - +
65K ILE* 4.2 19.3 - - + -
106K ILE* 4.3 18.4 - - + -
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Residues in contact with VAL 34 (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 ALA* 5.1 5.2 - - + -
33K LEU* 1.3 75.8 - - - +
35K MET* 1.3 65.2 + - - +
37K ASN* 5.1 2.2 - - - -
38K GLU* 3.0 18.8 - - - +
40K LEU* 3.7 19.7 - - + +
41K PHE* 3.7 6.2 - - - -
63K TYR* 5.2 0.7 - - - -
64K THR* 3.2 52.8 + - + +
66K GLY 5.7 0.7 - - - +
73K LEU* 5.5 6.5 - - + -
82K MET* 4.8 17.0 - - + -
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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