Contacts of the strand formed by residues 42 - 49 (chain A) in PDB entry 2O6E
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 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A ASP* 3.3 3.1 - - - -
39A VAL* 2.8 34.6 + - + +
40A GLY 3.2 0.8 - - - -
41A PRO* 1.3 91.8 - - + +
43A HIS* 1.3 58.7 + - - +
44A VAL* 3.9 12.1 + - + -
75A ILE* 3.8 23.3 - - + -
76A HIS 3.4 2.5 - - - +
78A ASN* 3.4 7.2 + - - -
86A TYR* 6.1 1.3 - - + -
92A VAL* 4.0 21.3 - - + -
95A LEU* 4.2 0.7 - - + -
144A ILE* 3.7 33.4 - - + -
167A TRP* 4.1 20.0 - - + -
171A LEU* 3.7 27.4 - - + -
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Residues in contact with HIS 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ASP* 3.0 42.9 + - + +
37A ARG 3.4 4.4 + - - -
38A ASP* 2.8 32.5 + - - +
42A LEU* 1.3 72.5 - - - +
44A VAL* 1.3 60.3 + - - +
45A GLY* 5.1 1.1 - - - -
74A ASP 3.4 4.6 - - - +
75A ILE* 3.5 2.1 - - - +
76A HIS* 2.8 61.0 + + + +
77A ALA 5.2 0.2 - - - +
78A ASN* 4.3 7.8 - - + +
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Residues in contact with VAL 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ASP* 3.4 4.1 - - - +
37A ARG* 2.7 42.5 + - - +
39A VAL* 4.1 12.1 - - + -
42A LEU* 3.9 17.7 - - + -
43A HIS* 1.3 78.6 - - - +
45A GLY* 1.3 69.2 + - - +
73A ALA* 4.7 0.7 - - + -
74A ASP 3.5 2.9 - - - -
75A ILE* 4.3 15.5 - - + -
142A PHE* 4.0 17.5 - - + -
144A ILE* 3.6 27.6 - - + -
173A ALA* 3.8 23.3 - - + -
175A TRP* 4.4 4.1 - - + -
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Residues in contact with GLY 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ASP* 3.5 22.2 - - - -
43A HIS* 4.3 1.8 - - - -
44A VAL* 1.3 81.0 - - - +
46A GLY* 1.3 58.3 + - - -
47A VAL* 5.5 0.9 - - - -
72A GLU 3.7 0.2 - - - +
73A ALA* 3.3 5.7 - - - -
74A ASP* 2.9 43.0 + - - -
175A TRP* 4.6 0.9 - - - -
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Residues in contact with GLY 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A PRO* 3.9 1.4 - - - +
33A ILE* 2.9 32.2 + - - +
34A GLY 4.3 5.2 + - - +
36A ASP* 4.6 2.4 + - - -
45A GLY* 1.3 75.2 - - - -
47A VAL* 1.3 67.8 + - - +
72A GLU 3.3 7.4 - - - -
142A PHE* 4.0 14.1 - - - -
175A TRP* 4.2 13.0 - - - -
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Residues in contact with VAL 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A GLU* 3.8 33.7 - - + +
31A PHE 3.2 15.9 - - - +
32A PRO* 4.6 2.9 - - + -
33A ILE* 3.7 5.3 - - - +
45A GLY 5.5 0.4 - - - -
46A GLY* 1.3 81.5 - - - +
48A TYR* 1.3 62.0 + - - +
49A PHE* 4.1 9.9 - - + -
71A ILE* 3.4 6.8 - - - +
72A GLU* 2.9 58.2 + - + +
74A ASP* 4.0 13.9 + - - +
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Residues in contact with TYR 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A PHE* 2.9 60.1 + + + +
32A PRO 3.5 9.9 - - - -
33A ILE* 4.1 5.2 - - + -
47A VAL* 1.3 75.5 - - - +
49A PHE* 1.3 67.0 + - - +
69A CYS* 4.3 12.6 - - + -
70A HIS 3.1 12.6 - - - +
71A ILE* 3.9 15.9 - - + -
178A PHE* 3.5 38.4 - + + -
179A GLU 4.4 7.4 + - - -
180A TRP* 4.2 15.1 - + - -
181A LYS* 4.4 11.6 + - - +
182A GLY 4.9 1.2 + - - -
184A GLN* 4.0 16.4 - - + +
185A TRP* 3.9 28.5 - + - -
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Residues in contact with PHE 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A PHE* 3.7 14.4 - + + -
29A ASP 3.3 20.9 - - - +
30A GLU* 3.6 28.3 - - + -
31A PHE* 4.4 3.8 - - + -
47A VAL* 4.1 5.6 - - + -
48A TYR* 1.3 81.1 - - - +
50A GLN* 1.3 78.4 + - + +
52A VAL* 3.6 25.4 - - + -
69A CYS* 3.3 7.4 - - - +
70A HIS* 2.9 35.2 + + + -
72A GLU* 3.2 43.1 - - + -
185A TRP* 3.6 17.5 - - - -
155B HIS* 4.0 2.9 - + - -
160B THR* 4.0 18.6 - - + -
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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