Contacts of the strand formed by residues 27 - 33 (chain C) in PDB entry 5DPW
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 ILE 27 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A PHE* 5.1 0.9 - - + -
20C ARG* 4.5 9.9 - - - +
26C LYS* 1.3 72.8 - - - +
28C PRO* 1.3 78.9 - - + +
29C VAL* 4.7 1.3 - - + -
48C PHE 3.7 0.2 - - - +
49C LEU* 3.7 1.2 - - - -
50C VAL* 2.6 55.0 + - + +
51C PRO 3.6 4.5 - - - +
52C GLN* 3.6 36.8 - - + +
91C MET* 4.0 21.3 - - + +
92C ALA* 4.1 2.2 - - - +
95C TYR* 3.5 43.3 - - + -
105C VAL* 4.3 12.3 - - + -
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Residues in contact with PRO 28 (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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16C VAL* 4.5 11.0 - - + -
19C ILE* 4.5 10.8 - - + -
20C ARG* 4.4 13.5 - - + +
26C LYS 3.9 5.6 - - - +
27C ILE* 1.3 91.1 - - + +
29C VAL* 1.3 60.0 + - - +
48C PHE 3.6 5.2 - - - +
49C LEU* 4.5 2.9 - - + -
95C TYR* 4.6 2.0 - - + -
103C GLY 3.3 26.7 - - - +
104C PHE* 3.6 17.7 - - + -
105C VAL* 3.0 26.7 + - - +
6D TRP* 3.9 18.4 - - + -
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Residues in contact with VAL 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 ILE* 4.1 2.7 - - + +
28C PRO* 1.3 77.4 - - - +
30C VAL* 1.3 66.7 + - - +
31C VAL* 4.0 10.1 - - + -
46C THR 3.7 0.5 - - - +
47C LYS* 3.4 5.9 - - - +
48C PHE* 2.8 44.3 + - + +
50C VAL* 3.5 30.3 - - + -
59C PHE* 3.9 22.2 - - + -
91C MET* 4.1 11.2 - - + -
104C PHE* 4.6 1.1 - - - -
105C VAL* 3.4 27.1 - - + +
107C MET* 4.0 12.8 - - + -
6D TRP* 4.8 0.4 - - - -
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Residues in contact with VAL 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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3C PHE* 3.7 31.2 - - + -
29C VAL* 1.3 73.8 - - - +
31C VAL* 1.3 59.7 + - - +
32C GLU* 3.7 21.1 - - + -
46C THR* 3.6 11.9 - - - +
47C LYS* 5.4 3.8 - - + -
104C PHE* 3.6 34.8 - - + -
105C VAL 2.9 8.7 + - - -
106C TYR* 3.6 29.0 - - + +
107C MET 2.8 34.7 + - - +
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Residues in contact with VAL 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 VAL* 4.0 6.3 - - + -
30C VAL* 1.3 73.4 - - - +
32C GLU* 1.3 63.6 + - - +
43C LEU* 3.4 28.5 - - + +
46C THR* 3.0 24.9 + - - +
48C PHE* 3.4 32.8 - - + -
59C PHE* 3.8 15.9 - - + -
63C ILE* 3.6 22.0 - - + -
77C LEU* 4.5 9.2 - - + -
107C MET* 3.4 8.5 - - + +
109C TYR* 3.6 15.7 - - + -
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Residues in contact with GLU 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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1C ARG 5.1 3.1 - - - +
2C PRO* 3.0 15.8 - - + +
3C PHE* 2.3 39.7 + - + +
4C LYS* 4.2 1.4 + - - +
30C VAL* 3.7 18.6 - - + -
31C VAL* 1.3 76.6 - - - +
33C ARG* 1.3 63.8 + - - +
46C THR* 5.8 2.7 - - - -
106C TYR* 4.3 14.3 - - - +
107C MET 2.9 13.4 + - - +
108C THR* 3.2 13.0 + - + +
109C TYR* 2.9 35.4 + - - -
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Residues in contact with ARG 33 (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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32C GLU* 1.3 77.5 - - - +
34C TYR* 1.3 70.8 + - - +
35C PRO* 3.2 9.7 - - - +
37C GLU* 2.6 51.2 + - + +
38C THR* 3.4 10.3 + - - +
40C LEU 2.0 34.8 + - - -
41C PRO 3.4 11.2 - - - -
42C PRO* 3.4 20.3 - - + +
108C THR* 3.5 3.7 - - - +
109C TYR* 3.4 35.8 + - + +
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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