Contacts of the helix formed by residues 106 - 117 (chain P) in PDB entry 6D84
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 ASN 106 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95P PHE* 3.5 35.3 - - + -
101P GLU 4.5 2.0 + - - -
102P SER* 3.3 32.4 + - - +
105P ASP* 1.3 79.5 - - - +
107P PHE* 1.3 54.5 + - - +
108P VAL* 3.1 12.9 + - - +
109P ILE* 3.5 11.0 + - + +
110P ILE* 3.4 16.9 - - - +
137P GLN* 4.7 6.4 - - - +
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Residues in contact with PHE 107 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35F LYS* 4.2 8.3 - - + -
38F ILE* 3.6 30.7 - - + +
39F ALA* 3.8 24.5 - - + -
42F THR* 4.4 15.9 - - + +
17P ILE* 5.5 1.6 - - + -
103P ILE 3.6 14.0 + - - +
104P ARG 3.3 27.1 - - - -
105P ASP* 3.4 15.0 + - - -
106P ASN* 1.3 72.0 - - - +
108P VAL* 1.3 75.0 + - + +
109P ILE 3.4 0.2 - - - -
110P ILE* 4.2 9.0 + - - +
111P TYR* 3.2 36.2 - - + -
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Residues in contact with VAL 108 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35F LYS* 3.4 30.3 - - + +
38F ILE* 5.5 2.7 - - + -
64F GLU* 3.3 30.5 - - + +
68F LEU* 4.5 11.3 - - + +
105P ASP 5.2 3.8 - - - +
106P ASN* 3.1 4.1 + - - +
107P PHE* 1.3 98.3 - - + +
109P ILE* 1.3 63.1 + - + +
111P TYR* 4.7 1.7 + - - +
112P GLU* 3.5 22.1 + - - +
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Residues in contact with ILE 109 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94P TYR* 6.0 3.4 - - + -
95P PHE* 4.1 17.5 - - + -
106P ASN* 3.5 12.3 - - + +
108P VAL* 1.3 82.3 - - + +
110P ILE* 1.3 68.9 + - + +
111P TYR 3.4 0.9 - - - -
112P GLU* 3.1 12.5 + - - +
113P LEU* 2.9 37.2 + - + +
135P ILE* 3.8 24.9 - - + +
136P THR* 3.8 31.6 - - - +
137P GLN* 3.9 23.6 - - + +
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Residues in contact with ILE 110 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17P ILE* 3.8 23.1 - - + -
91P PHE* 3.9 28.5 - - + -
95P PHE* 3.7 16.8 - - + -
102P SER 3.3 26.0 - - - +
103P ILE* 4.2 24.2 - - + +
106P ASN 3.4 17.9 + - - +
107P PHE* 4.2 2.6 + - - +
108P VAL 3.6 0.8 - - - -
109P ILE* 1.3 82.7 - - + +
111P TYR* 1.3 60.7 + - - +
113P LEU* 3.2 10.0 + - + +
114P LEU* 2.9 33.2 + - + +
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Residues in contact with TYR 111 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F ILE* 5.0 5.2 - - + -
41F MET* 4.9 4.5 + - + +
42F THR* 3.1 47.3 + - + +
68F LEU* 6.6 0.7 - - + -
71F LEU* 3.5 48.3 - - + +
75F ASN* 5.5 1.3 - - - -
17P ILE* 3.5 35.6 - - + +
18P CYS* 3.6 21.7 + - - -
19P ARG* 4.4 7.9 + - - -
107P PHE* 3.2 33.7 - + + +
108P VAL 5.0 2.5 - - - +
109P ILE 3.4 0.2 - - - -
110P ILE* 1.3 77.0 - - - +
112P GLU* 1.3 58.7 + - + +
114P LEU* 3.4 7.6 + - + +
115P ASP* 2.9 29.3 + - - +
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Residues in contact with GLU 112 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64F GLU* 3.6 34.3 - - - +
67F LYS* 3.5 38.8 - - + +
68F LEU* 4.0 5.7 - - + +
108P VAL* 3.5 22.3 - - - +
109P ILE* 3.1 17.1 + - - +
111P TYR* 1.3 75.8 - - + +
113P LEU* 1.3 60.2 + - - +
115P ASP* 3.3 7.1 + - - +
116P GLU* 2.9 30.9 + - - +
135P ILE* 4.7 18.2 - - + +
136P THR 5.3 3.1 - - - +
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Residues in contact with LEU 113 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91P PHE* 3.6 31.9 - - + -
94P TYR* 3.7 35.2 - - + -
95P PHE* 5.9 2.2 - - + -
109P ILE* 2.9 34.1 + - + +
110P ILE* 3.2 17.9 + - + +
112P GLU* 1.3 76.2 - - - +
114P LEU* 1.3 57.8 + - - +
116P GLU* 3.2 4.3 + - - +
117P LEU* 2.9 38.4 + - + +
131P LEU* 3.8 18.6 - - + -
135P ILE* 3.8 22.9 - - + -
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Residues in contact with LEU 114 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6P VAL* 4.9 17.3 - - + +
8P VAL* 6.0 2.2 - - + -
17P ILE* 4.3 30.7 - - + -
19P ARG* 3.9 31.0 - - + -
21P TYR* 2.7 26.0 + - - +
83P PHE* 5.7 3.4 - - + -
87P VAL* 4.7 13.2 - - + -
91P PHE* 4.0 24.2 - - + -
110P ILE* 2.9 24.1 + - + +
111P TYR* 3.9 5.6 - - + +
113P LEU* 1.3 73.2 - - - +
115P ASP* 1.3 63.7 + - - +
117P LEU* 4.7 7.9 - - + +
118P MET* 3.5 11.3 + - - +
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Residues in contact with ASP 115 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F LEU* 6.6 0.2 - - + -
74F MET* 4.2 7.8 - - - +
105F LEU* 3.7 19.2 - - - +
108F ARG* 3.4 29.4 + - - +
19P ARG* 2.5 35.5 + - - +
111P TYR 2.9 18.5 + - - +
112P GLU* 3.6 8.0 - - - +
113P LEU 3.2 0.2 - - - -
114P LEU* 1.3 76.3 - - - +
116P GLU* 1.3 63.8 + - - +
118P MET 2.9 16.3 - - - +
119P ASP* 3.1 14.9 - - - +
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Residues in contact with GLU 116 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67F LYS* 5.5 2.8 + - - -
101F LEU* 4.5 3.8 - - - +
105F LEU* 6.1 0.2 - - - +
108F ARG* 4.2 8.1 + - - +
136F TYR* 2.7 39.6 + - - -
112P GLU 2.9 17.5 + - - +
113P LEU* 3.2 4.2 + - - +
115P ASP* 1.3 79.9 - - - +
117P LEU* 1.3 60.8 + - - +
124P GLN* 2.8 36.8 + - - +
125P THR* 4.7 7.9 - - - +
131P LEU* 3.8 17.7 - - + -
134P TYR* 3.2 36.5 + - + +
135P ILE* 5.0 6.6 - - + +
153P VAL* 5.1 0.7 - - - +
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Residues in contact with LEU 117 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83P PHE* 3.6 16.1 - - + -
86P LYS* 6.1 0.7 - - + -
87P VAL* 3.9 28.9 - - + -
90P VAL* 5.0 8.5 - - + -
91P PHE* 4.7 15.9 - - + -
113P LEU* 2.9 25.1 + - + +
114P LEU* 4.7 5.8 - - + +
116P GLU* 1.3 76.0 - - - +
118P MET* 1.3 59.0 + - - +
123P PRO* 3.4 6.9 - - - +
124P GLN* 3.3 23.9 + - - +
125P THR 3.3 23.1 - - - +
126P THR* 3.8 21.3 - - + +
131P LEU* 3.9 24.7 - - + -
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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