Contacts of the strand formed by residues 40 - 48 (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 LEU 40 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32K ALA* 3.8 17.7 - - + -
33K LEU 3.2 27.6 - - - +
34K VAL* 3.7 8.9 - - + +
38K GLU* 1.3 97.0 - - + +
41K PHE* 1.3 62.4 + - - +
42K CYS 3.3 20.2 - - - +
43K SER* 5.1 1.6 - - - +
73K LEU* 4.1 23.6 - - + +
141K TRP* 4.3 27.1 - - + -
151K MET* 4.3 14.8 - - + +
193K GLY* 3.7 26.1 - - - +
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Residues in contact with PHE 41 (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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33K LEU* 3.0 36.4 + - + -
34K VAL 3.7 7.6 - - - -
35K MET* 3.4 40.6 - - + -
38K GLU* 4.9 0.9 - - - +
40K LEU* 1.3 81.1 - - - +
42K CYS* 1.3 104.0 + - + +
58K CYS* 3.4 19.7 - - - -
60K GLN* 3.8 25.8 - - + -
63K TYR* 4.6 5.2 - + + -
64K THR 6.2 0.2 - - - -
193K GLY* 4.3 15.5 + - - -
195K SER* 4.9 1.6 - - - -
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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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33K LEU* 2.5 45.0 + - + +
40K LEU* 3.3 9.0 - - - +
41K PHE* 1.3 109.8 - - + +
43K SER* 1.4 55.8 + - - +
57K HIS* 4.8 3.8 - - - -
58K CYS* 2.1 52.5 - - + -
193K GLY 4.8 2.2 - - - -
195K SER* 3.8 13.9 - - - -
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Residues in contact with SER 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* 3.6 18.2 + - - -
31K ALA 3.0 13.0 + - - -
33K LEU* 3.9 6.3 - - - +
40K LEU* 5.1 0.7 - - - +
42K CYS* 1.4 75.3 - - - +
44K GLY* 1.3 59.4 + - - +
54K SER* 2.9 19.6 + - - -
140K GLY* 4.5 5.5 - - - -
141K TRP* 3.9 14.7 - - - -
193K GLY 4.5 8.9 + - - -
194K ASP 4.6 1.3 + - - -
195K SER 3.1 7.6 + - - +
196K GLY* 3.2 10.3 - - - +
197K GLY* 3.8 23.6 - - - -
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Residues in contact with GLY 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 3.6 0.5 - - - +
30K GLN* 3.8 2.1 - - - -
31K ALA* 2.7 39.4 + - - -
33K LEU* 4.0 1.1 - - - +
43K SER* 1.3 76.7 - - - +
45K VAL* 1.3 68.7 + - - +
52K VAL* 3.9 7.0 - - - -
53K LEU 3.0 13.7 - - - -
54K SER* 4.1 2.0 - - - -
196K GLY 3.6 4.5 - - - -
198K PRO* 4.9 1.7 - - - +
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Residues in contact with VAL 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* 3.5 9.9 - - + +
44K GLY* 1.3 79.5 - - - +
46K LEU* 1.3 60.0 + - - +
47K VAL* 3.1 7.8 + - + -
52K VAL* 4.0 3.1 - - - +
53K LEU* 2.6 43.3 + - + +
121K ILE* 3.4 31.9 - - + -
198K PRO* 3.5 34.3 - - + -
209K LEU* 3.6 28.5 - - + -
212K LEU* 4.2 11.4 - - + -
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Residues in contact with LEU 46 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28K PRO 5.0 0.2 - - - +
29K TRP* 2.9 20.5 + - - +
31K ALA* 4.8 0.6 - - - +
44K GLY 4.2 0.2 - - - -
45K VAL* 1.3 68.2 - - - +
47K VAL* 1.3 57.9 + - - +
48K HIS 2.9 27.8 - - - +
49K PRO* 4.3 3.1 - - + +
51K TRP 3.3 9.2 - - - +
52K VAL* 3.9 16.9 - - + +
67K LEU* 4.3 14.8 - - + -
108K LEU* 4.1 14.1 - - + -
112K VAL* 4.1 12.8 - - + -
114K GLU* 5.8 3.1 - - + -
118K ILE* 4.0 27.6 - - + -
119K ARG 4.3 12.1 - - - +
120K SER* 3.2 12.4 - - - +
121K ILE* 3.0 25.5 + - - +
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Residues in contact with VAL 47 (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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45K VAL* 3.1 10.9 + - + +
46K LEU* 1.3 74.6 - - - +
48K HIS* 1.3 64.8 + - + +
51K TRP* 3.2 14.4 + - + +
53K LEU* 3.8 26.7 - - + +
105K LEU* 4.3 14.4 - - + -
120K SER* 4.1 6.4 + - - -
121K ILE 3.7 14.9 - - - +
122K SER* 5.7 0.3 - - - -
123K ILE* 3.7 33.2 - - + -
209K LEU* 3.8 16.8 - - + -
238K ILE* 5.2 1.1 - - + -
242K VAL* 5.1 4.7 - - + -
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Residues in contact with HIS 48 (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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236G GLU* 5.7 3.3 + - - -
46K LEU* 2.9 24.5 + - - +
47K VAL* 1.3 84.0 - - + +
49K PRO* 1.3 97.0 - - + +
50K GLN* 2.7 27.0 + - + -
51K TRP* 3.2 34.4 + + + +
120K SER* 3.8 7.0 - - - -
242K VAL* 3.7 24.2 + - + +
243K GLN* 5.5 5.5 + - - -
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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