Contacts of the helix formed by residues 107 - 116 (chain B) in PDB entry 5JRE
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 ASP 107 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A PRO* 5.6 1.2 - - - +
71A MET* 3.6 21.1 - - + +
73B TYR* 2.7 32.8 + - - -
101B LYS* 4.4 1.6 - - - +
106B VAL* 1.3 78.4 - - - +
108B THR* 1.3 63.0 - - - +
109B TRP* 2.9 9.9 + - - +
110B VAL* 2.7 35.6 + - - +
111B TYR* 3.1 19.5 + - - +
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Residues in contact with THR 108 (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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8A LEU* 3.8 23.6 - - + -
11A GLU* 3.9 11.9 - - + +
12A TYR* 4.2 21.8 - - + +
15A LEU* 3.9 17.8 - - + +
101B LYS* 3.1 32.4 + - - +
107B ASP* 1.3 75.5 - - - +
109B TRP* 1.3 61.8 + - - +
111B TYR* 3.5 2.2 + - - +
112B LEU* 3.1 34.7 + - + +
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Residues in contact with TRP 109 (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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12A TYR* 3.7 28.0 - + - -
15A LEU* 3.9 22.2 - - + +
16A GLU* 3.5 28.3 - - - -
19A LYS* 4.8 5.8 - - + -
71A MET* 4.0 31.1 + - + +
72A PHE* 3.9 31.1 - + - -
73B TYR* 4.3 1.1 - + - +
77B PHE* 3.7 27.4 - + - -
107B ASP* 2.9 8.4 + - - +
108B THR* 1.3 75.6 - - - +
110B VAL* 1.3 64.8 + - - +
111B TYR 3.3 0.3 + - - -
112B LEU* 3.3 5.0 + - - +
113B PHE* 3.2 50.6 + + - -
159B ASN* 3.9 24.2 - - + -
162B LEU* 4.9 1.8 - - + -
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Residues in contact with VAL 110 (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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73B TYR* 3.6 11.0 - - + +
77B PHE* 3.4 36.5 - - + +
80B LEU* 4.1 33.7 - - + +
81B GLN* 4.5 3.6 - - - +
84B VAL* 3.9 11.9 - - + +
106B VAL* 3.6 31.2 - - + -
107B ASP* 2.7 20.2 + - - +
109B TRP* 1.3 72.4 - - - +
111B TYR* 1.3 64.3 + - - +
113B PHE* 3.5 2.4 + - - +
114B GLY* 3.0 21.0 + - - -
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Residues in contact with TYR 111 (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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2A LEU* 4.1 5.7 - - + +
3A PRO* 3.9 16.9 + - - +
8A LEU* 4.0 38.4 - - + -
84B VAL* 3.9 12.1 - - + +
98B ILE* 3.9 8.0 - - - +
99B PRO 2.7 30.1 + - - -
100B SER* 3.7 2.3 - - - -
101B LYS* 3.5 36.8 - - + -
104B LEU* 4.2 9.6 - - + -
106B VAL* 4.0 5.2 - - + -
107B ASP 3.1 18.0 + - - +
108B THR* 3.5 5.2 - - - +
109B TRP 3.2 0.2 - - - -
110B VAL* 1.3 81.4 - - - +
112B LEU* 1.3 63.3 + - + +
114B GLY* 3.3 1.0 + - - -
115B ILE* 2.8 57.9 + - + +
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Residues in contact with LEU 112 (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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2A LEU* 5.1 2.0 - - + -
8A LEU* 4.0 26.9 - - + -
12A TYR* 3.5 45.5 - - + -
108B THR* 3.1 27.5 + - + +
109B TRP* 4.0 4.3 - - - +
111B TYR* 1.3 79.2 - - + +
113B PHE* 1.3 62.4 + - - +
115B ILE* 3.9 4.0 - - + +
116B GLY* 2.9 27.2 + - - -
152B LEU* 4.6 14.0 - - + +
155B ILE* 4.0 15.7 - - + -
157B LEU* 4.6 6.7 - - + -
162B LEU* 3.9 21.1 - - + +
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Residues in contact with PHE 113 (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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77B PHE* 3.7 29.4 - + + -
81B GLN* 3.5 17.0 + - + -
109B TRP* 3.2 55.7 + + - +
110B VAL 3.8 3.4 - - - +
112B LEU* 1.3 78.8 - - - +
114B GLY* 1.3 61.7 + - - +
116B GLY 3.5 4.9 + - - -
117B ASP* 3.4 19.1 - - - +
159B ASN* 3.6 24.0 - - - -
161B ASP* 3.8 26.5 - - + -
162B LEU* 3.7 24.0 - - + -
165B LYS* 3.7 22.1 - - - +
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Residues in contact with GLY 114 (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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81B GLN* 3.6 28.2 - - - +
84B VAL* 4.0 11.4 - - - -
85B GLU* 3.8 5.3 - - - +
110B VAL 3.0 14.7 + - - -
111B TYR 3.7 2.5 - - - -
113B PHE* 1.3 74.8 - - - +
115B ILE* 1.3 63.9 + - - +
117B ASP* 3.1 18.9 + - - +
118B ILE* 3.8 9.2 - - - +
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Residues in contact with ILE 115 (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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2A LEU* 3.8 24.2 - - + -
84B VAL* 4.2 4.3 - - + -
88B ALA* 4.1 18.4 - - + -
98B ILE* 3.6 28.9 - - + -
99B PRO* 4.9 0.4 - - + +
111B TYR* 2.8 55.8 + - + +
112B LEU* 3.9 6.1 - - + +
114B GLY* 1.3 67.5 - - - +
116B GLY* 1.3 59.4 + - - +
117B ASP 3.0 10.8 + - - -
118B ILE* 3.2 26.1 + - + +
119B ALA 4.8 0.2 + - - -
148B LEU* 4.0 18.5 - - + +
152B LEU* 4.6 8.5 - - + -
169B VAL* 5.8 0.3 - - - +
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Residues in contact with GLY 116 (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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112B LEU 2.9 18.9 + - - -
114B GLY 3.2 0.6 - - - -
115B ILE* 1.3 76.6 - - - +
117B ASP* 1.3 62.7 + - - +
119B ALA 5.0 0.8 + - - -
152B LEU* 5.0 12.6 - - - -
162B LEU* 6.0 0.2 - - - -
165B LYS* 3.7 35.3 - - - +
168B TYR* 3.7 14.4 - - - -
169B VAL* 4.5 5.7 - - - +
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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