Contacts of the helix formed by residues 27 - 37 (chain C) in PDB entry 6YOV
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 27 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19C SER* 4.5 4.3 - - - -
25C GLN 3.6 1.3 - - - +
26C PHE* 1.3 90.7 - - + +
28C VAL* 1.3 54.5 + - - +
29C GLY 3.1 2.9 - - - -
30C ARG* 2.7 57.3 + - + +
31C VAL* 3.0 17.3 + - + +
38D TYR* 4.6 8.1 - - + -
41D TYR* 3.6 44.4 - - + +
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Residues in contact with VAL 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C ARG* 3.9 32.1 - - + +
19C SER* 3.8 17.4 - - - +
22C ALA* 4.2 7.0 - - + -
24C LEU* 3.9 12.6 - - + -
26C PHE 2.8 18.4 + - - +
27C PRO* 1.3 70.3 - - - +
29C GLY* 1.3 63.3 + - - +
31C VAL* 3.1 10.7 + - - +
32C HIS* 3.0 21.8 + - - +
49C PRO* 3.7 2.1 - - + +
50C VAL* 3.8 33.2 - - + +
53C ALA* 3.8 18.2 - - + -
122D TYR* 5.2 0.2 - - + -
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Residues in contact with GLY 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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18C ARG* 3.7 30.7 + - - +
19C SER 5.4 0.2 - - - +
27C PRO 3.0 1.4 + - - -
28C VAL* 1.3 78.5 - - - +
30C ARG* 1.3 60.7 + - - +
32C HIS* 3.3 6.8 - - - +
33C ARG* 3.3 17.7 + - - +
30I A 4.2 15.2 + - - -
31I T 3.7 12.0 + - - -
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Residues in contact with ARG 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C PRO* 2.7 34.7 + - + +
29C GLY* 1.3 70.8 - - - +
31C VAL* 1.3 60.6 + - - +
32C HIS 3.1 1.6 - - - -
33C ARG* 2.9 17.7 + - + +
34C LEU* 2.7 49.7 + - + +
36D GLU* 3.5 34.4 - - - +
37D SER 3.1 25.1 + - - -
38D TYR* 3.8 20.3 - - - -
40D ILE* 5.9 0.2 - - - +
41D TYR* 3.9 23.0 + - - -
30I A 3.5 22.1 + - - +
123J G 5.6 3.4 + - - -
124J C 4.8 9.1 + - - -
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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
----------------------------------------------------------
26C PHE* 5.4 1.8 - - + -
27C PRO* 3.0 25.0 + - + +
28C VAL 3.1 7.2 + - - +
30C ARG* 1.3 75.6 - - - +
32C HIS* 1.3 56.7 + - - +
34C LEU* 3.2 14.8 + - + +
35C LEU* 2.8 30.6 + - + +
49C PRO* 3.6 28.7 - - + +
52C LEU* 3.9 26.9 - - + -
53C ALA* 4.1 17.5 - - + -
56C LEU* 4.7 10.3 - - + -
38D TYR* 6.1 2.5 - - + -
71D PHE* 4.2 4.9 - - + -
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Residues in contact with HIS 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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18C ARG* 3.7 32.1 + - - +
28C VAL 3.0 7.6 + - - +
29C GLY 3.3 11.2 - - - +
31C VAL* 1.3 77.1 - - - +
33C ARG* 1.3 59.9 + - + +
35C LEU* 3.3 4.5 + - - +
36C ARG* 2.8 66.0 + - - +
44C VAL* 3.9 27.6 - - + +
45C GLY 4.1 4.8 + - - -
46C ALA* 5.5 2.4 - - - -
49C PRO* 3.3 23.3 - - + +
114J A 4.5 2.2 - - - -
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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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29C GLY 3.3 8.6 + - - +
30C ARG* 2.9 17.2 + - + +
32C HIS* 1.3 84.1 - - + +
34C LEU* 1.3 72.7 + - - +
36C ARG* 3.3 12.7 + - + +
37C LYS* 3.1 42.5 + - + +
301C PTD 5.5 1.4 - - - +
36D GLU* 4.1 25.2 + - - -
29I A 5.1 11.2 + - - +
30I A 3.6 26.7 + - - +
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Residues in contact with LEU 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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30C ARG* 2.7 43.0 + - + +
31C VAL* 3.6 11.9 - - + +
33C ARG* 1.3 79.5 - - - +
35C LEU* 1.3 56.8 + - - +
37C LYS* 2.8 31.1 + - - +
40C TYR* 3.9 2.9 - - - -
301C PTD 4.4 23.8 - - + -
35D LYS* 6.0 4.7 - - - -
36D GLU* 6.0 2.0 - - - +
38D TYR* 3.5 27.8 - - + +
71D PHE* 3.4 34.8 - - + -
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Residues in contact with LEU 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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31C VAL* 2.8 19.9 + - + +
32C HIS 3.7 3.1 - - - +
34C LEU* 1.3 75.0 - - - +
36C ARG* 1.3 65.6 + - - +
37C LYS 3.2 6.8 - - - +
40C TYR* 3.6 19.8 + - + +
41C SER* 4.7 2.1 + - - -
44C VAL* 3.8 21.0 - - + +
48C ALA* 4.0 15.0 - - + -
49C PRO* 3.7 36.6 - - + -
52C LEU* 3.8 18.2 - - + -
71D PHE* 3.8 8.1 - - + -
75D ALA* 3.7 31.0 - - + -
90D ILE* 5.7 8.6 - - + +
95D ILE* 4.7 8.1 - - + -
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Residues in contact with ARG 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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32C HIS* 2.8 48.5 + - - +
33C ARG* 3.3 15.2 - - - +
34C LEU 3.2 0.2 - - - -
35C LEU* 1.3 79.1 - - - +
37C LYS* 1.3 59.4 + - + +
39C ASN* 4.4 6.4 + - - +
41C SER 4.4 11.9 - - - +
42C GLU 5.1 5.6 + - - +
44C VAL* 3.8 14.5 - - + +
114J A 3.2 44.5 + - - +
115J C 4.4 13.7 + - - -
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Residues in contact with LYS 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C ARG* 3.1 36.2 + - + +
34C LEU* 2.8 20.6 - - - +
35C LEU 3.2 1.9 - - - +
36C ARG* 1.3 75.5 - - + +
38C GLY* 1.3 68.6 + - - +
39C ASN* 3.2 6.5 + - - +
40C TYR* 3.2 15.1 - - - -
301C PTD 1.3 81.1 - - + +
83H HIS* 4.3 6.9 - - + +
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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