Contacts of the helix formed by residues 25 - 33 (chain T) in PDB entry 5IY8
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 LYS 25 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118S VAL* 5.6 2.8 - - - +
119S THR* 2.8 34.4 + - - -
120S GLU* 3.9 10.2 + - - +
121S ASN* 2.7 25.1 + - - +
122S THR 3.8 12.3 - - - +
123S SER* 3.4 17.5 - - - +
23T VAL 3.7 1.0 + - - -
24T PRO* 1.3 71.4 - - - +
26T TYR* 1.3 57.1 + - - +
28T SER* 2.7 20.8 + - - +
29T GLN* 2.8 22.4 + - + +
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Residues in contact with TYR 26 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121S ASN 4.7 0.2 + - - -
24T PRO* 3.1 3.9 - - + +
25T LYS* 1.3 76.9 - - - +
27T LEU* 1.3 64.5 + - - +
29T GLN* 3.7 8.4 - - + +
30T GLN* 3.1 37.3 + - + +
124T TYR* 4.2 20.6 - + - +
127T LEU* 3.4 47.6 - - + +
128T LYS* 5.7 7.0 - - + +
131T GLN* 3.4 29.4 - - + +
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Residues in contact with LEU 27 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23T VAL* 4.1 14.6 - - + -
24T PRO* 3.0 22.9 + - + +
26T TYR* 1.3 79.2 - - - +
28T SER* 1.3 57.8 + - - +
30T GLN* 3.3 8.8 + - + +
31T TRP* 3.0 72.8 + - + +
56T PHE* 5.0 1.3 - - + -
58T LEU* 4.3 7.4 - - + -
81T HIS* 3.7 35.4 - - + +
83T PHE* 6.4 0.2 - - + -
116T CYS* 4.1 20.4 - - - -
124T TYR* 5.3 0.6 + - - +
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Residues in contact with SER 28 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123S SER* 4.4 4.8 + - - -
125S TYR* 3.4 39.0 + - - -
23T VAL* 5.0 1.1 - - - +
24T PRO 3.2 4.9 + - - -
25T LYS* 2.7 31.7 + - - +
27T LEU* 1.3 78.2 - - - +
29T GLN* 1.3 57.8 + - - +
31T TRP* 3.3 15.3 + - - +
32T ALA* 2.8 26.5 + - - +
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Residues in contact with GLN 29 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25T LYS* 2.8 23.2 + - + +
26T TYR* 3.7 11.9 - - + +
27T LEU 3.3 0.2 - - - -
28T SER* 1.3 71.7 + - - +
30T GLN* 1.3 66.2 + - - +
32T ALA* 3.2 22.6 + - + +
33T LYS* 3.6 14.9 + - - +
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Residues in contact with GLN 30 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26T TYR* 3.1 30.9 + - + +
27T LEU* 3.5 13.5 - - + +
29T GLN* 1.3 75.7 - - - +
31T TRP* 1.3 63.6 + - + +
33T LYS* 3.3 46.9 + - - +
58T LEU* 4.6 20.0 - - + -
62T LEU* 3.3 53.0 - - + +
63T ALA* 5.0 2.3 - - - -
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Residues in contact with TRP 31 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16S VAL* 5.8 0.7 - - + -
18S VAL* 4.3 24.6 - - + +
125S TYR* 4.0 28.3 - + - -
127S PHE* 4.7 17.5 - + - -
23T VAL* 4.1 17.5 - - + -
27T LEU* 3.0 47.0 + - + +
28T SER* 3.4 18.6 - - - +
29T GLN 3.2 0.2 - - - -
30T GLN* 1.3 75.9 - - + +
32T ALA* 1.3 63.5 + - - +
33T LYS 3.1 0.7 - - - -
34T ALA* 3.1 21.3 + - - +
35T SER 3.8 1.9 + - - -
36T GLY 5.2 0.9 + - - -
40T VAL* 3.6 35.0 - - + +
56T PHE* 3.6 27.4 - + - -
58T LEU* 3.7 20.8 - - + +
62T LEU* 3.9 13.5 - - + -
83T PHE* 6.1 1.6 - + - -
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Residues in contact with ALA 32 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20S LYS* 6.0 0.5 - - - -
28T SER 2.8 14.0 + - - +
29T GLN* 3.2 23.1 + - - +
31T TRP* 1.3 76.2 - - - +
33T LYS* 1.3 57.4 + - + +
34T ALA 3.2 0.2 - - - -
35T SER* 3.1 23.0 + - - +
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Residues in contact with LYS 33 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29T GLN* 3.8 14.6 - - - +
30T GLN* 3.3 47.6 + - - +
31T TRP 3.1 1.2 - - - -
32T ALA* 1.3 74.5 - - - +
34T ALA* 1.3 64.7 + - - +
35T SER* 3.3 5.4 + - - -
62T LEU* 3.9 10.1 - - + +
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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