Contacts of the strand formed by residues 25 - 30 (chain A) in PDB entry 4OBP
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 PHE 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A PRO* 2.9 20.0 + - + +
22A ALA* 4.8 0.9 - - - -
23A GLY 4.8 1.4 + - - -
24A ILE* 1.3 83.1 + - + +
26A GLU* 1.3 62.3 + - - +
43A ARG 3.3 18.2 - - - -
44A HIS* 3.6 35.7 - + + -
45A VAL* 3.9 3.7 - - - +
51A ALA* 3.8 13.9 - - + -
53A ILE* 3.9 16.2 - - + -
86A TYR* 4.5 15.5 - + + -
89A PHE* 3.5 36.3 - + - -
102A TRP* 3.5 20.3 - - + -
104A VAL* 3.6 30.5 - - + -
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Residues in contact with GLU 26 (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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25A PHE* 1.3 75.6 - - - +
27A LEU* 1.3 68.2 + - - +
42A GLY* 3.2 4.5 - - - -
43A ARG* 2.8 83.5 + - + +
45A VAL* 3.8 24.7 - - + +
53A ILE* 4.0 1.6 - - - +
102A TRP* 4.3 3.4 - - - -
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Residues in contact with LEU 27 (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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26A GLU* 1.3 75.7 - - - +
28A VAL* 1.3 62.9 + - - +
40A TYR* 3.8 50.0 - - + -
41A LYS 4.0 2.2 - - - -
42A GLY* 4.4 0.2 - - - -
43A ARG* 5.6 0.5 + - - -
53A ILE* 3.9 25.6 - - + -
55A VAL* 4.1 7.6 - - + -
100A GLN* 5.3 3.4 - - - +
102A TRP* 3.5 39.4 - - + +
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Residues in contact with VAL 28 (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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26A GLU 4.4 0.2 - - - +
27A LEU* 1.3 76.3 - - - +
29A GLU* 1.4 69.9 + - + +
40A TYR* 5.3 0.2 - - - -
41A LYS* 2.8 43.5 + - + +
42A GLY 4.0 17.7 - - - +
43A ARG* 3.7 44.0 - - + +
50A LEU* 4.9 2.0 - - + -
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Residues in contact with GLU 29 (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 VAL* 1.4 89.2 - - + +
30A VAL* 1.4 68.7 + - + +
31A VAL* 5.4 1.6 - - + -
40A TYR* 3.3 11.6 - - - -
41A LYS* 2.7 63.3 + - + +
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Residues in contact with VAL 30 (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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29A GLU* 1.4 83.0 - - + +
31A VAL* 1.3 62.9 + - - +
32A GLY 4.2 0.7 + - - -
33A ASN* 4.3 27.9 + - + +
34A GLY 5.7 0.9 - - - +
37A GLY 4.8 7.2 - - - +
38A GLN* 4.6 8.7 - - - +
39A VAL 3.3 11.0 - - - +
40A TYR* 3.5 33.3 - - + +
38B GLN* 4.6 19.1 - - - +
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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