Contacts of the strand formed by residues 26 - 30 (chain A) in PDB entry 4DOH
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 LYS 26 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A LEU* 1.3 73.9 - - - +
27A THR* 1.3 75.0 + - - +
28A LEU* 3.4 6.6 + - + +
35A ILE 3.6 0.2 - - - +
36A ALA* 3.5 3.1 - - - -
37A THR* 2.8 51.7 + - - +
39A LEU* 3.6 29.6 - - + +
172A MET 3.5 12.3 + - - +
173A GLU* 3.5 38.1 + - - +
175A THR* 3.4 9.9 + - - -
176A GLU 2.5 31.4 + - - -
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Residues in contact with THR 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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25A LEU* 3.9 4.3 + - - +
26A LYS* 1.3 92.1 + - - +
28A LEU* 1.3 58.0 + - - +
29A ASN* 3.5 27.9 + - - +
34A VAL* 4.3 10.7 - - + +
35A ILE 3.7 6.2 + - - -
36A ALA* 4.8 7.8 - - - +
176A GLU* 3.7 3.2 - - - +
34C VAL* 4.2 33.6 + - + +
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Residues in contact with LEU 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 LYS* 3.4 5.6 + - + +
27A THR* 1.3 73.7 - - - +
29A ASN* 1.3 61.8 + - - +
30A LEU* 3.6 15.1 + - + +
33A CYS 3.8 0.2 - - - +
34A VAL* 3.4 10.2 - - - +
35A ILE* 2.9 46.6 + - + +
37A THR* 3.2 38.1 - - + +
71A LEU* 5.2 1.6 - - + -
83A LEU* 4.6 14.8 - - + -
119A ILE* 5.5 0.2 - - + -
172A MET* 3.4 35.2 - - + +
175A THR* 2.9 30.3 - - + +
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Residues in contact with ASN 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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27A THR* 3.5 24.9 + - - +
28A LEU* 1.3 75.4 - - - +
30A LEU* 1.3 66.5 + - - +
31A GLY 3.6 5.6 - - - +
33A CYS 4.3 0.9 - - - -
34A VAL* 4.7 12.8 - - + +
79A ARG* 3.2 24.0 + - - +
175A THR* 3.7 8.2 + - - -
176A GLU* 3.2 44.5 + - - +
34C VAL* 4.9 6.1 - - - +
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Residues in contact with LEU 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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28A LEU* 4.2 24.0 - - + +
29A ASN* 1.3 79.6 - - - +
31A GLY* 1.3 62.1 + - - +
32A SER 3.2 0.7 + - - -
33A CYS* 2.8 41.4 + - + +
35A ILE* 4.4 10.8 - - + -
71A LEU* 4.4 13.9 - - + -
76A PRO 3.5 9.2 - - - +
77A ALA* 5.1 1.4 - - - +
79A ARG* 4.0 20.4 - - + -
80A CYS* 3.7 25.3 - - + +
83A LEU* 4.3 12.3 - - + -
123A LEU* 3.5 32.1 - - + -
131A THR 4.5 1.7 - - - +
175A THR* 5.0 0.7 - - - +
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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