Contacts of the strand formed by residues 31 - 36 (chain C) in PDB entry 5Y39
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 PRO 31 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ALA* 4.4 16.2 - - + +
88A TYR* 3.3 20.3 - - - +
89A SER* 5.6 0.2 + - - -
23C VAL* 4.6 5.2 - - + -
24C VAL 3.5 8.7 - - - +
25C SER* 4.1 2.9 - - - -
29C GLY 3.3 8.4 - - - +
30C VAL* 1.4 90.7 - - + +
32C VAL* 1.3 60.2 + - - +
33C ILE 4.5 2.7 - - - +
34C LYS* 4.3 39.3 - - + +
45C LEU 5.3 2.2 - - - +
47C PRO* 5.4 7.4 - - + -
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Residues in contact with VAL 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A TYR* 4.0 18.1 - - + +
89A SER* 5.5 0.7 + - - -
92A LEU* 3.4 17.4 - - + +
24C VAL* 2.5 21.8 + - + +
25C SER* 4.3 5.4 - - - -
30C VAL 3.6 0.2 + - - -
31C PRO* 1.3 75.8 - - - +
33C ILE* 1.3 75.5 + - + +
88C LEU* 4.0 11.2 - - + -
117C LEU* 4.5 13.9 - - + +
120C VAL* 3.9 30.1 - - + -
121C VAL* 3.8 29.4 - - + -
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Residues in contact with ILE 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LEU* 3.6 32.3 - - + -
3C ASP* 5.3 0.2 - - - +
5C LEU* 4.1 10.8 - - + -
6C LYS* 3.8 28.9 - - + -
9C LEU* 4.4 21.3 - - + -
22C ILE 4.6 0.7 - - - +
23C VAL* 3.4 4.9 - - - +
24C VAL* 2.8 51.7 + - + +
31C PRO* 4.5 2.0 - - - -
32C VAL* 1.3 94.2 - - + +
34C LYS* 1.3 63.7 + - - +
35C VAL* 4.2 2.0 - - + -
117C LEU* 3.7 24.9 - - + -
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Residues in contact with LYS 34 (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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6C LYS* 3.0 27.4 + - - +
10C TYR* 4.5 2.3 + - - -
22C ILE 3.8 2.7 - - - -
23C VAL* 3.8 18.8 - - + -
31C PRO* 4.3 27.2 - - + +
33C ILE* 1.3 75.8 - - - +
35C VAL* 1.3 66.6 + - - +
36C ALA* 4.3 6.6 + - + -
42C GLU* 5.6 3.0 + - - -
45C LEU* 3.8 43.9 + - + +
46C ARG* 5.5 0.6 - - - +
47C PRO* 6.2 0.6 - - - +
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Residues in contact with VAL 35 (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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6C LYS* 3.4 42.4 - - + +
9C LEU* 3.5 35.0 - - + +
10C TYR* 3.7 26.0 - - + -
13C LEU* 4.3 3.9 - - + +
21C ALA* 3.3 3.1 - - - +
22C ILE* 2.9 54.3 + - + +
33C ILE* 4.2 1.1 - - + -
34C LYS* 1.3 76.6 - - - +
36C ALA* 1.3 62.8 + - - +
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Residues in contact with ALA 36 (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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10C TYR* 3.0 28.4 + - - +
13C LEU* 4.4 0.9 - - - -
20C HIS 3.4 6.7 - - - +
21C ALA* 3.7 16.4 - - + -
34C LYS* 4.2 8.5 + - + -
35C VAL* 1.3 76.1 - - - +
37C ASN* 1.3 67.8 + - - +
38C ASP* 4.9 1.9 - - - +
40C ALA* 4.4 0.7 - - + -
45C LEU* 3.9 24.9 - - + -
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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