Contacts of the helix formed by residues 94 - 104 (chain B) in PDB entry 4Y2H
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 GLY 94 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91B ALA* 2.8 21.8 + - - -
92B GLY 3.2 1.6 + - - -
93B THR* 1.3 78.9 - - - +
95B ILE* 1.3 64.8 + - - +
96B LEU 3.2 2.7 - - - -
97B SER* 3.1 11.3 + - - -
98B ILE* 3.0 29.8 + - - +
110B ALA* 5.5 1.6 - - - -
120B ALA* 4.1 11.4 - - - -
124B VAL* 5.4 4.0 - - - -
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Residues in contact with ILE 95 (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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211A VAL* 4.5 9.6 - - + -
215A TYR* 4.5 4.7 - - + -
217A VAL* 4.0 20.4 - - + -
219A MET* 4.2 20.8 - - - +
61B ILE* 4.2 14.8 - - + -
66B ARG* 4.8 2.5 - - - +
67B THR* 4.4 8.7 - - + -
93B THR* 3.4 16.6 + - - +
94B GLY* 1.3 75.5 - - - +
96B LEU* 1.3 62.5 + - + +
98B ILE* 3.1 11.6 + - - +
99B PHE* 3.0 56.2 + - + -
401B SAH 3.6 32.5 - - - +
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Residues in contact with LEU 96 (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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66B ARG* 5.4 1.8 - - - +
67B THR* 5.2 4.3 - - + -
70B TYR* 3.7 43.5 - - + -
74B ILE* 4.0 6.2 - - + +
88B ASP* 3.7 16.3 + - - +
94B GLY 3.2 0.6 - - - -
95B ILE* 1.3 77.9 - - + +
97B SER* 1.3 66.7 + - - +
99B PHE* 3.2 31.1 + - + +
100B CYS* 3.0 27.3 + - - -
153B VAL* 4.6 6.5 - - + -
155B GLU* 3.9 16.8 - - + +
401B SAH 3.4 37.4 + - - +
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Residues in contact with SER 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ASP* 2.6 34.7 + - - +
91B ALA* 4.0 0.5 - - - +
94B GLY* 3.1 10.7 + - - -
96B LEU* 1.3 77.8 - - - +
98B ILE* 1.3 61.1 + - - +
100B CYS* 3.1 6.9 + - - +
101B ALA* 3.0 18.9 + - - +
108B VAL* 3.6 23.9 - - - +
110B ALA* 3.3 16.4 - - - +
133B VAL* 3.8 19.4 - - - +
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Residues in contact with ILE 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A VAL* 3.7 32.5 - - + -
94B GLY 3.0 16.2 + - - +
95B ILE 3.1 6.9 + - - +
97B SER* 1.3 74.2 - - - +
99B PHE* 1.3 65.3 + - - +
101B ALA* 3.1 6.0 + - - +
102B GLN* 2.8 36.0 + - - +
123B VAL* 3.7 30.7 - - + -
124B VAL* 4.5 22.4 - - + -
127B ASN* 4.4 6.5 - - - +
129B LEU* 3.6 30.1 - - + -
133B VAL* 4.9 2.5 - - + -
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Residues in contact with PHE 99 (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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215A TYR* 3.7 29.4 - + - -
217A VAL* 4.0 12.8 - - + -
67B THR* 3.8 22.9 - - + -
71B ARG* 3.7 43.1 - - + -
74B ILE* 3.7 18.5 - - + +
75B LEU* 5.6 1.0 - - - +
95B ILE* 3.0 38.6 + - + -
96B LEU* 3.2 29.8 + - + +
98B ILE* 1.3 75.7 - - - +
100B CYS* 1.3 57.0 + - - +
102B GLN* 3.3 16.8 + - - +
103B ALA* 2.9 28.9 + - - +
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Residues in contact with CYS 100 (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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74B ILE* 4.0 23.3 - - - -
81B LEU* 4.9 5.2 - - + +
86B VAL* 3.8 22.4 - - + -
96B LEU 3.0 18.4 + - - -
97B SER* 3.4 10.3 - - - +
98B ILE 3.1 0.2 - - - -
99B PHE* 1.3 73.4 - - - +
101B ALA* 1.3 64.5 + - - +
103B ALA* 3.2 10.7 + - - +
104B GLY 3.3 0.7 + - - -
105B ALA* 3.1 23.2 + - - +
108B VAL* 3.8 14.1 - - + -
153B VAL* 3.8 28.0 - - - -
185B LEU* 6.1 0.7 - - - -
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Residues in contact with ALA 101 (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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97B SER 3.0 12.9 + - - +
98B ILE* 3.4 10.1 - - - +
100B CYS* 1.3 74.5 - - - +
102B GLN* 1.3 62.7 + - - +
104B GLY* 3.1 4.7 + - - -
105B ALA 4.2 4.5 - - - -
108B VAL* 4.0 4.8 - - + +
129B LEU* 4.3 12.1 - - + -
132B ARG* 2.7 49.0 + - + +
133B VAL* 3.9 20.6 - - + -
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Residues in contact with GLN 102 (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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215A TYR 4.6 2.8 - - - +
216A GLY* 2.8 30.0 + - - +
217A VAL* 4.2 2.0 - - - +
75B LEU* 5.2 5.0 - - + +
98B ILE* 2.8 40.8 + - + +
99B PHE* 3.7 25.1 - - - +
101B ALA* 1.3 74.7 - - + +
103B ALA* 1.3 60.2 + - - +
104B GLY* 3.1 1.8 + - - -
127B ASN* 5.5 1.2 + - - -
129B LEU* 5.3 5.5 - - + +
132B ARG* 5.1 0.4 - - - +
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Residues in contact with ALA 103 (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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74B ILE* 3.8 21.5 - - + +
75B LEU* 4.3 20.6 - - + +
78B TRP* 3.5 34.3 - - + +
81B LEU* 4.3 11.7 - - + -
82B ARG* 4.9 1.4 + - - +
99B PHE 2.9 13.1 + - - +
100B CYS 3.2 10.9 + - - +
102B GLN* 1.3 76.6 - - - +
104B GLY* 1.3 57.5 + - - +
105B ALA 3.8 0.2 - - - -
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Residues in contact with GLY 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B LEU 3.9 4.9 - - - -
82B ARG* 3.4 13.0 - - - +
83B GLY 2.9 22.9 + - - -
101B ALA 3.1 6.8 + - - -
102B GLN 3.1 5.3 - - - -
103B ALA* 1.3 79.1 - - - +
105B ALA* 1.3 64.7 + - - +
106B ARG* 3.5 0.3 + - - -
132B ARG* 3.6 6.3 + - - -
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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