Contacts of the strand formed by residues 45 - 52 (chain g) in PDB entry 5K0Y
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 ARG 45 (chain g).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41g VAL* 4.7 2.4 - - - +
42g THR* 3.0 40.3 + - - +
43g PRO 3.3 5.1 - - - +
44g THR* 1.4 78.4 - - - +
46g THR* 1.3 73.6 + - - +
47g GLU* 3.3 33.1 + - + +
82g GLY 5.7 0.2 - - - +
83g SER* 3.5 20.4 + - - +
85g GLU* 3.9 20.8 - - + +
87g TYR* 3.4 17.6 + - - -
107h GLU* 5.5 2.4 + - - -
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Residues in contact with THR 46 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39g VAL* 3.9 24.7 - - + -
40g ARG 4.2 4.5 - - - +
41g VAL* 5.4 4.5 - - + +
45g ARG* 1.3 74.2 + - - +
47g GLU* 1.4 64.0 + - - +
48g ILE* 5.8 1.1 - - + -
79g PHE* 3.6 36.6 - - + -
83g SER* 3.2 22.7 + - - +
84g VAL* 3.4 13.7 - - + +
85g GLU* 3.1 25.3 + - - +
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Residues in contact with GLU 47 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38g GLU 4.0 0.3 - - - +
39g VAL* 3.4 5.9 - - - +
40g ARG* 2.9 63.8 + - + +
42g THR* 3.5 22.9 - - - +
45g ARG* 3.3 40.4 + - + +
46g THR* 1.4 76.4 - - - +
48g ILE* 1.4 60.1 + - - +
49g ILE* 4.1 7.0 - - + -
85g GLU 3.6 4.0 - - - -
87g TYR* 3.3 34.5 - - + -
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Residues in contact with ILE 48 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21g LEU* 4.0 31.0 - - + -
25g LEU* 4.2 13.9 - - + -
37g VAL* 4.4 5.4 - - + -
38g GLU 3.6 3.6 - - - +
39g VAL* 4.1 15.3 - - + -
46g THR* 5.8 1.3 - - + -
47g GLU* 1.4 73.2 - - - +
49g ILE* 1.3 62.7 + - - +
50g ILE* 3.9 19.5 + - + -
70g THR* 4.9 1.6 - - + -
73g VAL* 5.2 12.8 - - + -
84g VAL* 4.0 18.6 - - + -
85g GLU 3.1 14.7 + - - +
86g LEU* 3.5 20.0 - - + +
87g TYR 3.2 20.8 + - - +
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Residues in contact with ILE 49 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37g VAL* 3.5 6.4 - - - +
38g GLU* 2.9 48.2 + - + +
40g ARG* 3.6 42.4 - - + +
47g GLU* 4.8 11.4 - - + +
48g ILE* 1.3 77.0 - - - +
50g ILE* 1.4 63.7 + - - +
51g LEU* 3.6 8.1 - - + +
87g TYR* 3.4 22.4 - - + +
88g ALA 4.8 0.7 - - - +
89g GLU* 3.9 30.5 - - + +
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Residues in contact with ILE 50 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25g LEU* 4.9 3.1 - - + -
29g LEU* 4.4 21.5 - - + -
34g TYR* 4.8 5.8 - - + -
36g GLY 4.4 2.0 - - - -
37g VAL* 3.6 25.4 - - + -
48g ILE* 3.9 20.6 - - + -
49g ILE* 1.4 69.4 - - - +
51g LEU* 1.4 64.3 + - - +
52g ALA* 3.3 10.8 + - + +
58g VAL* 3.9 31.2 - - + -
69g LEU* 5.5 1.6 - - + -
86g LEU* 3.6 40.2 - - + -
87g TYR 3.0 8.9 + - - +
88g ALA* 3.9 2.1 - - - +
89g GLU* 3.2 22.7 + - - +
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Residues in contact with LEU 51 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34g TYR* 4.3 1.4 - - - -
35g SER* 3.2 34.2 + - - -
36g GLY* 3.3 24.4 + - - +
37g VAL 3.9 14.4 - - - +
38g GLU* 4.0 11.4 - - + +
49g ILE* 3.6 20.6 - - + +
50g ILE* 1.4 69.8 - - - +
52g ALA* 1.3 58.3 + - - +
89g GLU* 3.9 19.7 - - + -
91g VAL* 4.6 19.3 - - + -
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Residues in contact with ALA 52 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32g ASP 4.1 7.6 - - - +
33g GLY 3.5 12.1 - - - +
34g TYR* 5.1 0.7 - - - +
35g SER* 4.5 0.7 - - - -
50g ILE* 4.1 8.7 - - + +
51g LEU* 1.3 74.1 - - - +
53g THR* 1.4 61.1 + - - +
54g ARG 3.2 4.5 - - - +
55g THR* 3.5 18.7 - - + +
58g VAL* 3.8 28.7 - - + -
89g GLU 3.0 18.9 + - - +
90g LYS* 3.8 7.6 - - - -
91g VAL* 4.2 4.0 + - - +
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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