Contacts of the helix formed by residues 107 - 116 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73C TYR* 2.6 33.4 + - - -
101C LYS* 4.4 0.7 - - - -
106C VAL* 1.3 79.3 - - - +
108C THR* 1.3 63.3 + - - +
109C TRP* 2.9 9.5 + - - +
110C VAL* 2.7 36.3 + - - +
111C TYR* 3.1 19.7 + - - +
70D PRO* 5.3 2.3 - - + +
71D MET* 3.4 20.1 - - + +
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Residues in contact with THR 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C LYS* 3.3 23.1 - - - +
107C ASP* 1.3 74.0 - - - +
109C TRP* 1.3 57.3 + - - +
111C TYR* 3.5 2.7 - - - +
112C LEU* 3.1 39.0 + - + +
8D LEU* 3.8 23.8 - - + -
11D GLU* 3.9 16.6 + - + +
12D TYR* 4.1 18.2 - - - +
15D LEU* 3.7 21.9 - - + +
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Residues in contact with TRP 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C TYR* 5.0 0.7 - + - -
77C PHE* 3.7 26.7 - + - -
107C ASP* 2.9 9.8 + - - +
108C THR* 1.3 76.0 - - - +
110C VAL* 1.3 64.2 + - - +
111C TYR 3.3 0.2 + - - -
112C LEU* 3.3 4.7 + - + +
113C PHE* 3.2 47.6 + + - -
159C ASN* 3.9 25.8 - - + -
162C LEU* 5.0 1.8 - - + -
12D TYR* 3.7 27.6 - + - -
15D LEU* 3.9 22.1 - - + +
16D GLU* 3.4 24.9 - - - -
19D LYS* 5.2 7.9 - - + -
71D MET* 3.9 31.9 + - + +
72D PHE* 4.1 30.9 - + - -
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Residues in contact with VAL 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C TYR* 3.6 11.2 - - + +
77C PHE* 3.4 38.1 - - + +
80C LEU* 4.1 32.8 - - + +
81C GLN* 4.4 3.8 - - - +
84C VAL* 3.9 11.9 - - + +
106C VAL* 3.6 31.0 - - + -
107C ASP* 2.7 20.6 + - - +
109C TRP* 1.3 72.5 - - - +
111C TYR* 1.3 63.6 + - - +
113C PHE* 3.5 2.8 + - - +
114C GLY* 3.0 20.3 + - - -
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Residues in contact with TYR 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C VAL* 3.9 13.3 - - + +
98C ILE* 3.9 10.9 - - - +
99C PRO 2.7 29.9 + - - -
100C SER* 3.8 4.9 - - - -
101C LYS* 3.5 35.0 - - + -
104C LEU* 4.3 9.4 - - + -
106C VAL* 4.0 4.9 - - + -
107C ASP 3.1 19.3 + - - +
108C THR 3.5 4.9 - - - +
109C TRP 3.2 0.2 - - - -
110C VAL* 1.3 79.9 - - - +
112C LEU* 1.3 66.0 + - + +
114C GLY* 3.3 1.4 + - - -
115C ILE* 2.8 56.2 + - + +
2D LEU* 4.2 9.6 - - + +
3D PRO* 4.0 12.0 + - - +
8D LEU* 4.2 29.8 - - + -
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Residues in contact with LEU 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C THR* 3.1 27.2 + - + +
109C TRP* 3.3 4.9 + - + +
111C TYR* 1.3 83.3 - - + +
113C PHE* 1.3 59.6 + - - +
115C ILE* 3.9 3.9 - - + +
116C GLY* 2.9 26.9 + - - -
152C LEU* 4.6 14.8 - - + +
155C ILE* 4.0 12.3 - - + -
157C LEU* 4.7 6.3 - - + -
162C LEU* 3.9 21.6 - - + +
2D LEU* 5.2 3.6 - - + -
8D LEU* 3.7 23.6 - - + -
12D TYR* 3.4 46.2 - - + -
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Residues in contact with PHE 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C PHE* 3.7 26.7 - + + -
81C GLN* 3.5 20.3 + - + -
109C TRP* 3.2 54.5 + + - +
110C VAL 3.8 4.0 - - - +
112C LEU* 1.3 79.8 - - - +
114C GLY* 1.3 61.2 + - - +
116C GLY 3.5 5.0 + - - -
117C ASP* 3.4 18.7 - - - +
159C ASN* 3.5 24.5 - - - -
161C ASP* 3.8 26.9 - - + -
162C LEU* 3.6 24.9 - - + -
165C LYS* 3.7 21.4 - - - +
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Residues in contact with GLY 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C GLN* 3.6 28.0 - - - +
84C VAL* 4.0 11.2 - - - -
85C GLU* 3.8 5.1 - - - +
110C VAL 3.0 14.5 + - - -
111C TYR 3.7 2.7 - - - -
113C PHE* 1.3 75.2 - - - +
115C ILE* 1.3 64.5 + - - +
117C ASP* 3.1 19.1 + - - +
118C ILE* 3.8 9.2 - - - +
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Residues in contact with ILE 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C VAL* 4.0 4.9 - - + +
88C ALA* 4.1 18.2 - - + -
98C ILE* 3.6 29.6 - - + -
99C PRO 5.0 0.2 - - - +
111C TYR* 2.8 55.0 + - + +
112C LEU* 3.9 7.0 - - + +
114C GLY* 1.3 71.6 - - - -
116C GLY* 1.3 62.9 + - - +
117C ASP 3.0 1.8 + - - -
118C ILE* 3.2 25.2 + - + +
119C ALA 4.8 0.2 + - - -
148C LEU* 3.9 19.0 - - + +
152C LEU* 4.7 8.0 - - + +
169C VAL* 5.8 0.2 - - - +
2D LEU* 3.8 24.7 - - + -
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Residues in contact with GLY 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C LEU 2.9 16.9 + - - -
113C PHE 3.5 0.2 + - - -
114C GLY 3.2 0.8 - - - -
115C ILE* 1.3 76.9 - - - +
117C ASP* 1.3 63.3 + - - +
119C ALA 5.0 0.8 + - - -
152C LEU* 5.0 13.4 - - - +
162C LEU* 5.9 0.2 - - - -
165C LYS* 3.6 35.9 - - - +
168C TYR* 3.8 14.2 - - - -
169C VAL* 4.5 5.5 - - - +
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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