Contacts of the helix formed by residues 61 - 69 (chain Y) in PDB entry 5MG3
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 61 (chain Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59Y THR* 3.8 15.1 + - - +
60Y ILE* 1.4 85.7 - - - +
62Y GLU* 1.3 67.5 + - - +
63Y MET* 4.0 8.1 - - - +
64Y PHE* 3.3 15.1 + - + +
65Y ASN* 3.1 17.5 + - - +
139Y LEU* 4.5 9.4 - - + -
140Y PRO* 5.9 0.9 - - + -
292Y SER* 3.8 33.2 - - - +
295Y GLY* 5.6 2.7 - - - -
301Y ASN* 4.2 18.4 - - + +
311Y GLN* 3.4 39.0 - - - +
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Residues in contact with GLU 62 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60Y ILE* 4.9 0.8 - - - +
61Y ILE* 1.3 75.6 - - - +
63Y MET* 1.4 67.9 + - - +
65Y ASN* 3.3 9.0 + - - +
66Y MET* 3.0 30.6 + - + +
314Y GLN* 3.1 30.8 + - + +
396Y LYS* 2.7 41.2 + - - +
400Y TYR 5.3 1.3 - - - +
401Y PHE* 3.8 16.7 - - + -
402Y GLY* 2.8 21.7 + - - -
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Residues in contact with MET 63 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61Y ILE* 3.3 11.6 - - - -
62Y GLU* 1.4 79.1 - - - +
64Y PHE* 1.3 61.6 + - - +
66Y MET* 4.2 7.6 + - - -
67Y PHE* 3.9 16.1 + - - +
285Y LEU* 4.8 4.0 - - + +
288Y ALA* 3.5 22.4 - - + -
289Y THR* 3.5 43.5 - - - +
292Y SER* 3.3 31.6 - - - +
293Y TRP* 4.9 0.3 - - - -
310Y LEU 4.0 5.2 - - - +
311Y GLN 3.5 22.4 - - - +
314Y GLN* 3.5 42.6 - - + +
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Residues in contact with PHE 64 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61Y ILE* 3.3 16.4 + - + +
62Y GLU 3.3 0.6 - - - -
63Y MET* 1.3 79.5 - - - +
65Y ASN* 1.3 69.4 + - - +
67Y PHE 3.9 0.2 - - - -
68Y SER* 2.9 62.2 + - - -
70Y GLY* 5.7 0.2 - - - -
71Y ALA* 4.0 21.1 - - - -
72Y LEU* 4.4 17.5 - - + -
74Y ARG 5.9 0.7 - - - -
75Y ALA* 6.2 3.8 - - + -
79Y ALA* 4.1 15.9 - - + -
135Y ILE* 3.9 36.8 - - + -
139Y LEU* 5.8 6.7 - - + -
292Y SER* 4.7 8.6 - - - +
293Y TRP* 3.7 35.6 - + + -
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Residues in contact with ASN 65 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60Y ILE* 3.3 27.5 - - - +
61Y ILE 3.1 16.3 + - - +
62Y GLU* 3.5 7.8 - - - +
64Y PHE* 1.3 81.7 - - - +
66Y MET* 1.3 62.0 - - - +
68Y SER* 3.3 8.8 + - - -
69Y GLY 3.2 22.3 + - - -
70Y GLY 3.8 7.7 - - - +
71Y ALA* 3.5 31.7 - - - +
72Y LEU 4.7 0.3 + - - -
400Y TYR* 2.9 30.9 + - - +
401Y PHE* 3.5 14.7 - - + -
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Residues in contact with MET 66 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62Y GLU* 3.0 24.5 + - - +
63Y MET* 4.3 10.3 - - - +
65Y ASN* 1.3 73.4 - - - +
67Y PHE* 1.3 77.0 + - + +
69Y GLY 4.6 1.9 + - - -
82Y ILE* 4.4 2.9 - - - +
195Y ILE* 4.7 3.1 - - - +
285Y LEU* 3.9 33.0 - - + -
314Y GLN* 4.9 7.6 - - - -
401Y PHE* 3.5 35.2 - - + -
402Y GLY 3.7 9.6 - - - +
403Y GLY* 3.7 6.7 - - - -
404Y THR* 3.5 28.9 - - - +
405Y SER* 2.8 41.2 + - - +
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Residues in contact with PHE 67 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63Y MET 3.9 16.2 + - - +
64Y PHE 3.6 1.8 + - - +
65Y ASN 3.2 0.2 - - - -
66Y MET* 1.3 90.3 - - + +
68Y SER* 1.4 55.3 + - - +
69Y GLY 3.7 0.2 - - - -
81Y GLY* 3.2 1.6 - - - -
82Y ILE* 2.7 58.6 + - + +
83Y MET* 3.4 30.8 + - + -
86Y ILE* 4.1 28.7 - - + -
278Y ILE* 5.6 5.4 - - + -
282Y SER* 4.4 9.6 - - - -
285Y LEU* 4.1 39.0 - - + -
286Y PHE* 5.2 2.2 - - + -
289Y THR* 4.1 17.7 - - + -
293Y TRP* 5.1 0.2 - - + -
404Y THR* 6.6 0.2 - - - -
405Y SER* 4.0 13.2 - - - -
408Y ILE* 5.9 0.9 - - + -
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Residues in contact with SER 68 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33Y PHE* 4.3 7.3 - - - -
37Y SER* 5.5 1.0 - - - -
64Y PHE* 2.9 44.8 + - - -
65Y ASN* 3.3 5.6 + - - -
67Y PHE* 1.4 71.2 - - - +
69Y GLY* 1.4 57.8 + - - +
70Y GLY* 3.0 30.5 + - - -
78Y PHE 4.4 3.1 - - - +
79Y ALA* 3.5 25.8 - - - -
80Y LEU 4.3 1.5 + - - -
81Y GLY* 3.3 24.9 + - - +
194Y GLY 5.4 0.2 - - - -
293Y TRP* 4.7 2.5 - - - -
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Residues in contact with GLY 69 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33Y PHE* 5.0 0.7 - - - -
37Y SER* 4.5 4.6 - - - +
65Y ASN 3.2 8.4 + - - -
66Y MET 4.6 2.6 + - - -
67Y PHE 3.7 2.4 - - - -
68Y SER* 1.4 75.3 - - - +
70Y GLY* 1.3 54.8 + - - +
74Y ARG* 3.6 10.4 + - - -
194Y GLY 4.9 8.7 + - - -
195Y ILE* 5.5 4.7 - - - +
197Y ALA* 3.0 34.7 - - - +
204Y ALA* 4.2 6.8 - - - +
401Y PHE* 4.6 11.4 - - - -
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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