Contacts of the strand formed by residues 28 - 32 (chain C) in PDB entry 5U0A
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 28 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C TRP* 1.3 116.9 - - + +
29C ILE* 1.3 63.5 + - - +
30C ALA 3.4 1.0 + - - -
41C MET* 3.2 1.1 - - - -
42C LEU* 2.8 41.4 + - + +
43C GLY 4.1 0.9 - - - +
44C LEU* 3.9 17.3 - - + -
47C VAL* 3.5 31.9 - - + -
57C VAL* 3.6 26.5 - - + -
58C GLU 4.9 0.9 - - - -
59C ILE* 4.5 8.1 - - + -
68C LEU* 4.5 11.7 - - + -
72C LEU* 5.4 7.2 - - + -
183C TRP* 5.5 0.2 - - - +
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Residues in contact with ILE 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C TRP 3.2 10.6 + - - +
28C LEU* 1.3 71.1 - - - +
30C ALA* 1.3 62.8 + - - +
31C ARG* 4.8 8.7 - - + +
39C PRO* 3.8 30.1 - - + +
40C GLU 3.9 4.7 - - - +
41C MET* 3.7 32.3 - - + -
57C VAL* 3.2 9.2 - - - +
58C GLU* 3.0 55.7 + - + +
60C PRO* 4.0 24.0 - - + -
183C TRP* 4.4 6.5 - - + +
215N SER* 6.2 0.4 - - - +
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Residues in contact with ALA 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ILE* 1.3 77.7 - - - +
31C ARG* 1.3 62.8 + - - +
32C SER 4.3 0.7 + - - -
39C PRO* 3.1 6.7 - - - +
40C GLU* 2.9 37.4 + - + +
42C LEU* 3.7 18.4 - - + -
54C LEU* 3.7 31.2 - - + +
56C ASP 3.8 4.0 - - - -
57C VAL* 3.9 6.3 - - + -
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Residues in contact with ARG 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ILE* 4.8 5.0 - - + +
30C ALA* 1.3 77.4 - - - +
32C SER* 1.3 62.4 + - - +
36C LEU* 5.4 14.3 + - + +
37C ALA* 6.0 0.2 - - - +
38C ALA 5.4 0.4 - - - +
39C PRO* 3.1 43.6 - - + +
54C LEU* 3.1 11.1 - - - +
55C SER* 2.8 25.9 + - - +
56C ASP* 3.0 21.9 + - + +
58C GLU* 3.1 27.2 + - + +
215N SER* 5.1 4.8 - - - -
216N THR* 2.7 42.5 + - - +
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Residues in contact with SER 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C ALA 4.2 0.8 + - - -
31C ARG* 1.3 77.7 - - - +
33C ARG* 1.3 64.6 + - - +
34C ASP* 2.7 40.7 + - - +
35C VAL* 4.9 0.9 - - - +
36C LEU* 4.2 13.9 + - - +
37C ALA 5.2 4.0 + - - -
39C PRO* 5.8 0.6 - - - +
53C GLU 4.4 1.8 - - - -
54C LEU* 3.7 17.8 - - - +
55C SER* 3.8 10.0 + - - -
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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