Contacts of the helix formed by residues 77 - 89 (chain J) in PDB entry 3MQT
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 GLU 77 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73J ARG* 6.0 1.9 - - - +
74J ASP* 3.2 21.3 + - + +
75J PRO 3.1 2.8 - - - -
76J LEU* 1.3 74.9 - - - +
78J PHE* 1.3 64.7 + - - +
80J ALA* 3.4 10.4 + - + +
81J ASN* 2.9 31.6 + - - +
84J ARG* 4.8 5.4 + - - -
122L TYR* 4.4 5.5 - - - -
123L LYS* 3.2 43.9 + - + +
126L GLY 3.4 17.7 - - - +
127L GLY* 3.6 22.1 - - - -
128L ALA* 3.8 8.9 + - - +
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Residues in contact with PHE 78 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75J PRO 3.1 22.2 - - - -
76J LEU* 3.0 27.3 + - + -
77J GLU* 1.3 72.2 - - - +
79J ARG* 1.3 58.4 + - + +
81J ASN* 4.0 2.8 - - - +
82J TYR* 2.9 31.7 + - - +
106J ASP* 4.7 2.9 - - - +
109J LEU* 3.6 27.4 - - + -
110J TYR* 3.4 58.8 - + - +
113J ALA* 3.7 18.8 - - + -
124J LEU* 3.8 24.7 - - + -
290J THR* 3.5 10.7 + - + +
126L GLY* 3.7 3.9 + - - -
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Residues in contact with ARG 79 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78J PHE* 1.3 77.7 - - + +
80J ALA* 1.3 59.8 + - - +
82J TYR* 3.8 0.4 - - - -
83J ASN* 2.8 42.4 + - - +
290J THR* 4.4 14.4 - - + -
294J ARG* 3.6 24.7 - - - +
79L ARG* 5.3 7.7 - - - +
125L MET 4.0 20.9 + - - -
126L GLY* 3.4 14.4 + - - +
129L GLN* 3.9 14.1 - - - +
293L LEU* 4.0 21.0 + - - +
296L MET* 4.2 20.2 - - - +
297L ASP* 2.8 40.6 + - - -
326L VAL* 5.2 0.7 - - - -
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Residues in contact with ALA 80 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77J GLU* 4.0 9.9 - - + +
79J ARG* 1.3 76.6 - - - +
81J ASN* 1.3 58.6 + - - +
83J ASN* 3.5 1.4 + - - +
84J ARG* 2.9 44.3 + - - +
126L GLY 3.0 16.8 + - - +
127L GLY 4.0 5.8 - - - -
128L ALA 3.7 13.5 - - - +
129L GLN* 3.7 29.1 - - + +
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Residues in contact with ASN 81 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7J ILE* 4.9 1.0 - - - +
69J ALA 4.5 0.6 + - - -
70J VAL* 4.0 18.1 - - + +
73J ARG* 3.7 18.3 - - - +
74J ASP 3.1 23.0 + - - +
75J PRO* 3.9 10.4 - - - +
77J GLU* 2.9 25.4 + - - +
78J PHE* 4.1 2.0 - - - +
80J ALA* 1.3 73.7 - - - +
82J TYR* 1.3 65.6 + - - +
84J ARG* 3.0 29.8 - - - +
85J MET* 3.0 29.7 + - - +
109J LEU* 4.2 14.5 - - + +
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Residues in contact with TYR 82 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78J PHE 2.9 23.8 + - - +
79J ARG 3.8 2.5 - - - +
81J ASN* 1.3 74.1 - - - +
83J ASN* 1.3 76.2 + - - +
85J MET* 3.3 11.1 + - - +
86J TYR* 3.0 39.5 + + + +
99J LEU* 3.7 19.9 - - - +
102J ILE* 3.6 21.3 - - + -
106J ASP* 4.4 7.1 + - + +
264J ARG* 4.6 7.4 - - - -
287J GLY 3.2 29.4 - - - -
290J THR* 3.8 25.6 - - + -
291J GLU* 3.3 38.7 + - + +
294J ARG* 6.3 1.8 - - - -
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Residues in contact with ASN 83 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79J ARG* 2.8 28.7 + - - +
80J ALA 3.9 2.9 - - - +
82J TYR* 1.3 87.8 - - - +
84J ARG* 1.3 56.7 + - - +
86J TYR* 4.5 2.9 - - - -
87J ASP* 2.9 45.8 + - - +
264J ARG* 5.5 4.2 + - - -
294J ARG* 5.8 1.4 + - - -
129L GLN* 2.6 33.5 - - + +
300L GLU* 5.9 0.2 + - - -
328L HIS* 3.7 17.6 + - - -
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Residues in contact with ARG 84 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68J GLU 5.2 0.4 - - - -
69J ALA* 2.8 48.3 + - + +
73J ARG* 3.6 44.5 - - - +
77J GLU* 4.8 4.4 + - - -
80J ALA* 2.9 35.4 + - - +
81J ASN* 3.0 28.3 + - - +
83J ASN* 1.3 74.0 - - - +
85J MET* 1.3 57.6 + - - +
87J ASP* 4.7 3.6 - - - -
88J THR* 2.7 49.6 + - + +
128L ALA 4.6 6.9 + - - -
129L GLN* 5.9 0.4 - - - +
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Residues in contact with MET 85 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66J ILE* 4.0 17.3 - - + +
69J ALA* 3.6 19.5 - - + +
70J VAL* 3.9 13.5 - - + -
81J ASN 3.0 24.6 + - - +
82J TYR* 3.7 14.1 - - + +
84J ARG* 1.3 78.6 - - - +
86J TYR* 1.3 60.3 + - - +
88J THR* 4.1 0.2 - - - -
89J THR* 2.8 31.9 + - - +
102J ILE* 4.1 31.9 - - + +
105J ILE* 3.7 47.3 - - + -
106J ASP* 4.3 9.6 - - + +
109J LEU* 4.3 7.2 - - + -
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Residues in contact with TYR 86 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82J TYR* 3.0 41.9 + + + +
83J ASN* 3.8 5.2 - - - +
85J MET* 1.3 76.8 - - - +
87J ASP* 1.3 73.4 + - - +
89J THR* 3.6 1.4 + - - -
90J LYS* 3.2 38.7 + - - +
94J MET* 3.0 45.1 + - + +
95J ARG* 3.0 13.2 + - - -
99J LEU* 4.0 14.6 - - + -
102J ILE* 3.9 11.8 - - + +
263J THR* 4.2 8.5 - - + -
265J PHE* 3.7 9.7 - + - -
239W ASP* 2.7 30.2 + - - -
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Residues in contact with ASP 87 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62J TRP* 3.6 15.7 - - + +
83J ASN* 2.9 31.0 + - - +
84J ARG* 4.1 3.4 - - - +
86J TYR* 1.3 86.6 - - - +
88J THR* 1.3 65.8 + - + +
89J THR 3.1 1.3 + - - -
90J LYS* 3.2 42.6 + - - +
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Residues in contact with THR 88 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61J LYS 4.1 6.7 - - - +
62J TRP 3.2 7.2 - - - -
64J ASN* 3.0 52.6 + - - +
65J ASN 5.1 1.4 + - - -
69J ALA* 3.6 16.5 - - + +
84J ARG* 2.7 39.7 + - + +
85J MET 3.6 2.8 + - - -
87J ASP* 1.3 78.5 - - + +
89J THR* 1.3 62.4 + - - +
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Residues in contact with THR 89 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53J PHE* 5.2 6.5 - - + -
62J TRP 3.3 3.6 - - - -
64J ASN 3.5 20.4 - - - +
66J ILE* 4.0 25.5 - - + +
85J MET* 2.8 23.0 + - - +
86J TYR 3.6 3.5 + - - -
88J THR* 1.3 86.1 - - - +
90J LYS* 1.3 56.3 + - - +
91J TRP 3.2 3.1 - - - -
92J ILE* 3.1 17.2 + - + +
93J GLY* 2.7 37.7 + - - -
94J MET 5.3 0.2 + - - -
98J GLY 5.7 0.3 + - - -
102J ILE* 4.1 11.8 - - - +
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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