Contacts of the helix formed by residues 61 - 71 (chain B) in PDB entry 5LXY
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 VAL 61 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B HIS* 3.9 16.6 - - + -
60B GLU* 1.3 78.8 - - + +
62B SER* 1.3 62.4 + - - +
63B VAL 3.4 0.3 + - - -
64B PRO* 3.5 12.0 - - - +
65B TYR* 3.9 6.2 + - - +
320C PRO* 3.6 26.2 - - + +
321C GLY* 3.8 23.6 - - - +
324C LYS* 4.2 15.9 - - - +
311D TYR* 4.7 2.8 - - - -
312D ARG* 3.6 37.5 - - + +
315D GLN* 5.3 3.4 + - - +
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Residues in contact with SER 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ALA 4.0 7.3 + - - +
34B GLY* 3.6 13.5 - - - -
35B PRO* 4.3 1.9 + - - +
57B PHE* 3.5 28.3 - - - +
59B HIS* 2.9 19.7 + - - +
61B VAL* 1.3 79.2 - - - +
63B VAL* 1.3 56.7 + - - +
65B TYR* 3.7 5.5 - - - +
66B ALA* 2.8 32.9 + - - +
320C PRO* 5.1 0.4 - - - -
321C GLY* 3.6 23.1 - - - +
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Residues in contact with VAL 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ASP 3.3 25.6 - - - +
10B ARG* 3.6 23.6 - - - +
11B THR 4.4 3.4 - - - +
12B LEU* 3.9 16.9 - - + +
57B PHE* 3.9 15.5 - - + -
60B GLU* 3.0 12.9 + - - +
62B SER* 1.3 78.4 - - - +
64B PRO* 1.3 69.7 - - + +
66B ALA* 3.7 2.1 - - - +
67B MET* 3.1 19.9 + - - +
84B PHE* 3.6 28.0 - - + -
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Residues in contact with PRO 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B GLU 3.1 14.8 - - - +
61B VAL* 3.5 11.4 - - - +
63B VAL* 1.3 94.7 - - + +
65B TYR* 1.3 61.6 + - - +
67B MET* 3.3 4.4 + - + +
68B ASN* 3.1 22.0 + - - +
84B PHE* 4.1 18.6 - - + -
311D TYR* 3.1 14.3 + - - +
315D GLN* 4.1 15.7 - - - +
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Residues in contact with TYR 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B GLN 4.8 0.7 - - - -
33B ALA* 3.6 27.6 - - + -
61B VAL 3.9 8.6 + - - +
62B SER* 3.5 8.3 + - - +
63B VAL 3.2 0.8 - - - -
64B PRO* 1.3 76.5 - - - +
66B ALA* 1.3 61.4 + - - +
68B ASN* 3.0 3.9 + - - +
69B LEU* 2.8 41.4 + - + +
313C MET* 3.1 28.5 + - + +
316C LEU* 3.6 25.0 - - + +
317C GLY 2.8 27.5 + - - -
319C PRO* 3.9 21.1 - - + -
320C PRO* 3.9 9.0 - - + -
311D TYR* 3.1 46.4 + + + -
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Residues in contact with ALA 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU* 3.9 9.9 - - + -
30B PHE* 4.1 7.9 - - + -
33B ALA* 3.6 18.4 - - + -
57B PHE* 3.5 29.6 - - + -
62B SER 2.8 19.3 + - - +
63B VAL 3.7 2.9 - - - +
65B TYR* 1.3 76.8 - - - +
67B MET* 1.3 62.7 + - - +
69B LEU* 4.5 0.9 - - - +
70B LEU* 2.9 28.6 + - - +
71B ASN 4.0 0.3 + - - -
82B ILE* 4.0 1.7 - - - +
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Residues in contact with MET 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B LEU* 4.4 1.0 - - - +
63B VAL 3.1 12.8 + - - +
64B PRO 3.4 10.1 - - - +
65B TYR 3.1 0.2 - - - -
66B ALA* 1.3 78.0 - - - +
68B ASN* 1.3 66.4 + - - +
71B ASN* 3.0 47.8 + - - +
82B ILE* 3.1 51.4 - - + +
83B GLN* 4.1 0.4 - - - -
84B PHE* 3.6 51.6 - - + +
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Residues in contact with ASN 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B PRO* 3.1 6.5 + - - +
65B TYR* 3.0 7.6 + - - +
67B MET* 1.3 85.7 - - - +
69B LEU* 1.3 63.9 + - - +
71B ASN* 4.5 3.6 + - - +
312C ARG* 4.0 19.9 + - - +
316C LEU* 4.1 22.4 - - + +
311D TYR* 3.0 31.6 + - + +
324F LYS* 5.8 1.9 - - - -
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Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B GLN* 4.4 4.7 - - + -
33B ALA* 4.3 15.0 - - + +
65B TYR* 2.8 33.2 + - + +
66B ALA* 4.2 0.7 - - - +
68B ASN* 1.3 79.4 - - - +
70B LEU* 1.3 81.3 + - + +
71B ASN 5.2 0.2 - - - -
73B ILE* 3.9 12.0 - - - +
309C PHE* 4.3 15.0 - - + -
312C ARG* 4.4 16.1 + - + +
313C MET* 3.6 46.2 - - + +
316C LEU* 4.1 18.1 - - + +
324F LYS* 4.9 4.7 + - - -
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Residues in contact with LEU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B LEU* 4.0 28.3 - - + +
30B PHE* 3.5 36.6 - - + -
33B ALA* 4.3 11.2 - - + -
66B ALA 2.9 14.6 + - - +
69B LEU* 1.3 94.9 - - + +
71B ASN* 1.3 68.0 + - - +
72B GLY 3.3 0.5 + - - -
73B ILE* 3.1 24.0 + - + +
80B ILE* 3.5 13.1 - - + +
82B ILE* 3.9 11.0 - - + -
309C PHE* 3.7 34.5 - - + -
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Residues in contact with ASN 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B MET* 3.0 43.9 + - - +
68B ASN 4.5 2.6 + - - +
69B LEU 3.8 0.6 - - - +
70B LEU* 1.3 77.5 + - - +
72B GLY* 1.3 64.0 + - - +
80B ILE 3.6 2.6 - - - +
81B LYS* 3.9 2.1 - - - -
82B ILE* 3.1 34.3 + - + +
324F LYS* 3.3 20.1 - - - +
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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