Contacts of the helix formed by residues 74 - 85 (chain J) in PDB entry 1YI2
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 ARG 74 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26750 A 4.0 30.3 + - - +
26760 C 3.0 20.5 + - - +
91B PRO 3.3 22.1 + - - -
92B TYR* 3.7 21.0 - - - +
73J LYS* 1.3 77.5 + - - +
75J PRO* 1.3 69.6 - - + +
76J ASP* 2.7 43.4 + - + +
77J GLY 3.4 3.0 + - - +
78J ILE* 2.9 22.5 + - - +
105J LEU* 3.9 9.1 - - - +
136J SER* 3.3 2.0 - - - -
141J ALA* 4.3 8.3 - - + -
142J ASN 4.5 10.1 - - - +
144J THR* 3.9 17.2 - - - +
145J TRP* 4.5 6.1 - - - -
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Residues in contact with PRO 75 (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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41J ALA* 3.9 5.1 - - - +
42J GLU* 3.8 21.5 - - + +
74J ARG* 1.3 82.4 - - + +
76J ASP* 1.3 62.4 + - - +
78J ILE* 3.9 2.9 - - + -
79J PHE* 3.4 18.5 + - - +
105J LEU* 3.3 24.2 - - + -
132J LEU* 3.4 40.7 - - + +
133J GLY* 4.6 0.4 - - - -
136J SER* 2.9 23.3 - - - +
145J TRP* 3.6 19.7 - - + -
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Residues in contact with ASP 76 (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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28150 G 4.8 4.6 + - - +
92B TYR* 3.9 15.8 + - - -
41J ALA* 4.8 3.1 - - - -
74J ARG* 2.7 41.4 + - + +
75J PRO* 1.3 86.3 - - - +
77J GLY* 1.3 62.5 + - - +
79J PHE* 3.7 0.3 + - - +
80J LYS* 3.4 17.4 + - - +
103J VAL* 3.2 38.3 - - - +
104J TYR* 3.9 7.1 + - - -
105J LEU* 3.8 16.3 - - - +
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Residues in contact with GLY 77 (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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72J PRO* 3.5 20.8 - - - +
74J ARG* 3.4 4.6 + - - +
76J ASP* 1.3 79.2 - - - +
78J ILE* 1.3 67.8 + - - +
80J LYS* 2.9 8.4 + - - +
81J ARG* 2.7 26.5 + - - +
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Residues in contact with ILE 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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12420 A 4.8 0.2 + - - -
19J MET* 3.5 18.6 - - + -
57J TYR* 3.8 28.5 - - + -
71J TYR* 3.5 20.1 + - + +
72J PRO* 3.0 34.8 - - - +
73J LYS 4.0 6.7 - - - +
74J ARG 2.9 28.7 + - - +
75J PRO* 4.0 2.9 - - + -
76J ASP 3.4 0.2 - - - -
77J GLY* 1.3 77.9 - - - +
79J PHE* 1.3 56.8 + - - +
81J ARG* 3.3 2.3 + - - +
82J THR* 2.6 31.5 + - - +
132J LEU* 3.8 14.1 - - + +
135J ILE* 5.2 4.7 - - + -
136J SER* 4.5 2.0 - - - +
139J LEU* 4.3 7.2 - - + -
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Residues in contact with PHE 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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14J ALA* 3.8 22.9 - - + -
19J MET* 3.5 40.1 - - + +
22J VAL* 3.7 31.9 - - + -
23J ALA* 4.0 11.2 - - + -
38J VAL* 3.8 15.5 - - + -
41J ALA* 4.4 9.0 - - + -
44J ALA* 3.8 19.3 - - + -
75J PRO 3.4 14.3 + - - +
76J ASP 4.0 2.9 - - - +
77J GLY 3.2 0.4 - - - -
78J ILE* 1.3 78.3 - - - +
80J LYS* 1.3 64.8 + - - +
82J THR* 3.2 2.7 + - - -
83J ILE* 3.1 37.4 + - + +
103J VAL* 4.0 11.9 - - + -
132J LEU* 4.3 1.1 - - + -
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Residues in contact with LYS 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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28150 G 2.6 57.0 + - + +
76J ASP 3.4 12.0 + - - +
77J GLY* 2.9 10.8 + - - +
79J PHE* 1.3 79.9 - - - +
81J ARG* 1.3 57.4 + - - +
83J ILE* 3.0 9.0 + - + +
84J ARG 2.9 23.2 + - - -
98J PHE* 3.5 42.0 + - + -
99J GLU* 5.3 2.6 + - - +
101J VAL* 3.2 28.1 + - + -
103J VAL* 4.0 15.0 - - + +
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Residues in contact with ARG 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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12410 G 4.8 1.8 - - - +
12420 A 5.5 2.7 - - - +
20810 A 4.5 14.1 + - - -
20820 G 3.1 16.0 + - - -
69J TYR* 4.8 5.9 + - - -
70J PHE* 2.7 47.6 + - - -
71J TYR* 4.0 27.8 - - + +
72J PRO* 4.1 13.4 - - + +
77J GLY 2.7 19.1 + - - +
78J ILE 3.8 3.4 - - - +
80J LYS* 1.3 73.1 - - - +
82J THR* 1.3 63.3 + - - +
84J ARG* 3.2 49.6 + - - +
85J GLY* 3.0 20.4 + - - +
98J PHE* 5.6 0.9 - - - -
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Residues in contact with THR 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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12410 G 2.7 24.2 + - - -
12420 A 3.1 51.0 + - - -
19J MET* 3.6 21.4 - - + -
23J ALA* 4.0 18.8 - - + -
78J ILE* 2.6 23.1 + - - +
79J PHE* 3.2 12.1 - - - -
81J ARG* 1.3 78.4 - - - +
83J ILE* 1.3 60.8 + - - +
85J GLY 3.5 0.3 + - - -
86J MET* 3.8 7.4 + - + +
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Residues in contact with ILE 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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23J ALA* 3.9 24.0 - - + +
26J VAL* 4.2 14.6 - - + -
27J ALA* 4.7 13.2 - - + -
38J VAL* 4.3 7.0 - - + -
79J PHE* 3.1 31.4 + - + +
80J LYS* 3.0 8.9 + - + +
82J THR* 1.3 73.8 - - - +
84J ARG* 1.3 56.4 + - - +
85J GLY 3.0 1.8 - - - -
86J MET* 2.7 30.8 + - - +
87J LEU* 3.4 23.8 + - + +
98J PHE* 4.6 7.9 - - + -
101J VAL* 4.1 28.7 - - + -
103J VAL* 4.3 7.2 - - + -
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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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20810 A 2.8 29.5 + - - -
20820 G 3.0 28.0 + - - -
80J LYS 2.9 7.4 + - - +
81J ARG* 3.2 48.2 + - - +
83J ILE* 1.3 77.2 - - - +
85J GLY* 1.3 57.3 + - - +
87J LEU* 3.0 31.1 + - - +
89J HIS* 3.4 47.7 + - + -
98J PHE* 3.6 39.0 - - + -
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Residues in contact with GLY 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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11040 C 4.8 1.6 + - - -
12400 G 2.9 23.7 + - - +
12410 G 3.3 30.3 - - - +
20810 A 5.6 5.6 - - - -
81J ARG* 3.0 13.1 + - - -
82J THR 3.5 0.4 + - - -
83J ILE 3.0 1.0 - - - -
84J ARG* 1.3 78.0 - - - +
86J MET* 1.3 56.0 + - - +
87J LEU 3.4 1.7 - - - +
89J HIS* 5.6 1.3 - - - -
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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