Contacts of the strand formed by residues 40 - 46 (chain H) in PDB entry 4BEI
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 ILE 40 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H PRO 5.3 1.1 - - - +
39H VAL* 1.3 80.1 - - - +
41H GLU* 1.3 72.0 + - - +
42H ALA 4.1 2.1 + - - +
64H ILE* 3.9 24.0 - - + -
65H ARG 3.5 7.0 - - - +
66H ASN* 4.9 2.5 - - + -
72H VAL* 3.8 29.8 - - + -
74H PHE* 4.0 24.2 - - + -
135H VAL* 4.2 16.6 - - + -
137H ALA* 4.5 8.3 - - + -
143H PHE* 3.2 52.3 - - + +
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Residues in contact with GLU 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39H VAL 4.3 0.2 + - - -
40H ILE* 1.3 73.9 - - - +
42H ALA* 1.3 61.9 - - - +
43H ASN* 3.7 25.1 + - - +
63H GLY 3.7 1.0 - - - +
64H ILE* 3.5 2.9 + - - -
65H ARG* 2.8 53.4 + - + +
67H GLU* 2.1 41.7 - - - +
111H MET* 5.1 0.2 - - - +
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Residues in contact with ALA 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40H ILE* 4.1 2.9 + - + -
41H GLU* 1.3 75.5 - - - +
43H ASN* 1.3 70.7 + - - +
63H GLY 3.4 6.7 - - - +
64H ILE* 4.7 0.9 - - + +
133H LEU* 4.2 14.6 - - + -
135H VAL* 4.2 19.7 - - + -
143H PHE* 4.6 10.3 - - + +
144H LYS* 4.4 14.4 - - - +
145H ALA* 3.5 16.3 - - + +
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Residues in contact with ASN 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41H GLU* 3.7 26.1 + - - +
42H ALA* 1.3 85.3 + - - +
44H LEU* 1.3 64.2 + - - +
61H GLN 4.4 0.7 - - - -
62H LEU* 3.7 0.2 - - - -
63H GLY* 2.9 32.9 + - - +
111H MET* 4.3 19.4 - - - +
133H LEU* 3.2 10.4 - - - +
145H ALA* 3.7 6.1 - - - -
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Residues in contact with LEU 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43H ASN* 1.3 80.2 - - - +
45H SER* 1.3 66.9 + - - +
46H LEU* 4.4 3.4 - - + -
60H SER* 3.9 16.2 - - - -
61H GLN 3.5 4.7 - - - +
62H LEU* 3.4 31.9 - - + -
78H LEU* 4.2 4.5 - - + -
131H VAL* 3.7 31.6 - - + +
133H LEU* 3.7 14.1 - - + +
145H ALA* 3.3 34.2 - - + +
147H GLN* 3.0 38.0 - - + +
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Residues in contact with SER 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44H LEU* 1.3 75.5 - - - +
46H LEU* 1.3 66.3 + - - +
47H ASN 4.2 0.2 + - - -
60H SER* 3.4 5.9 - - - -
61H GLN* 3.0 47.1 + - - +
147H GLN* 4.1 5.6 - - - -
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Residues in contact with LEU 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44H LEU* 4.4 7.6 - - + -
45H SER* 1.3 83.5 - - - +
47H ASN* 1.3 63.6 + - - +
48H GLN* 3.4 24.2 + - - +
49H ASN* 4.5 8.9 + - - +
58H ILE* 4.3 13.0 - - + -
59H SER 3.9 1.6 - - - -
60H SER* 3.9 17.7 - - - -
118H PHE* 5.0 0.2 - - + -
131H VAL* 4.3 15.0 - - + -
147H GLN* 3.6 25.5 - - + +
148H GLU 3.6 25.6 - - - +
149H PHE* 4.1 18.4 - - + -
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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