Contacts of the helix formed by residues 105 - 117 (chain H) in PDB entry 1DSX
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 PRO 105 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99E ARG* 3.3 40.2 - - + +
102E VAL* 6.0 5.4 - - + -
103H ASN 4.0 5.8 - - - +
104H VAL* 1.3 93.7 - - + +
106H LEU* 1.3 62.1 + - + +
107H ASP* 3.4 3.4 - - - +
108H ILE* 3.2 16.4 + - + -
109H PHE* 3.0 23.2 + - - +
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Residues in contact with LEU 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100H ARG* 3.0 56.5 - - + +
101H PRO 4.9 2.5 - - - +
104H VAL 3.8 13.2 - - - +
105H PRO* 1.3 73.6 - - + +
107H ASP* 1.3 56.2 + - - +
109H PHE* 4.3 5.6 - - + +
110H SER* 2.8 36.0 + - - -
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Residues in contact with ASP 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E ARG* 4.0 16.8 + - - +
99E ARG* 2.7 48.4 + - - -
105H PRO* 3.5 6.1 - - - +
106H LEU* 1.3 72.6 - - - +
108H ILE* 1.3 70.9 + - - +
110H SER* 4.0 4.6 - - - -
111H GLU* 3.3 20.6 + - - +
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Residues in contact with ILE 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90E TYR* 3.7 53.1 + - + +
97E ARG* 4.9 4.9 - - + +
99E ARG* 3.9 31.0 - - + +
81H ASN* 4.3 9.4 - - + +
84H SER* 4.3 6.7 - - - +
104H VAL* 3.9 14.1 - - + -
105H PRO* 3.2 22.2 + - + +
107H ASP* 1.3 91.3 + - - +
109H PHE* 1.3 62.1 + - - +
111H GLU* 3.2 15.0 + - - +
112H GLU* 3.3 13.9 + - + +
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Residues in contact with PHE 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84H SER* 3.5 43.1 - - - -
87H ALA* 3.5 22.4 - - + -
88H ILE* 4.0 17.3 - - + -
98H LEU* 4.3 10.5 - - + -
99H ARG 3.8 9.2 - - - -
100H ARG* 3.5 33.2 - - + -
101H PRO* 4.2 11.2 - - + -
104H VAL* 4.0 9.6 - - + +
105H PRO 3.0 16.3 + - - +
106H LEU* 4.0 6.3 - - - +
108H ILE* 1.3 77.9 - - - +
110H SER* 1.3 57.4 + - - +
112H GLU* 3.0 6.3 + - + +
113H ILE* 2.9 57.1 + - + +
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Residues in contact with SER 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100H ARG* 3.2 25.1 + - - -
106H LEU 2.8 23.2 + - - -
107H ASP* 4.0 5.4 - - - -
108H ILE 3.4 0.2 - - - -
109H PHE* 1.3 71.2 - - - +
111H GLU* 1.3 61.4 + - - +
113H ILE* 3.2 14.3 + - - +
114H ARG* 3.0 42.1 + - - +
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Residues in contact with GLU 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90E TYR* 5.1 7.9 - - - +
97E ARG* 5.7 6.0 + - - +
80H ARG* 4.2 14.4 + - - +
107H ASP 3.3 12.2 + - - +
108H ILE* 3.2 11.8 + - - +
109H PHE 3.2 0.8 - - - -
110H SER* 1.3 75.9 - - - +
112H GLU* 1.3 61.7 + - - +
114H ARG* 3.4 18.8 + - - +
115H PHE* 3.0 26.3 + - - +
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Residues in contact with GLU 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90E TYR* 4.9 8.7 + - - -
80H ARG* 2.8 49.5 + - - +
81H ASN* 4.4 19.1 + - + +
84H SER* 3.6 33.9 - - - +
88H ILE* 4.7 3.1 - - + -
108H ILE* 3.3 11.3 + - + +
109H PHE* 3.0 10.5 + - + +
111H GLU* 1.3 78.4 - - - +
113H ILE* 1.3 65.8 + - - +
115H PHE* 3.1 3.3 + - - +
116H TYR* 2.9 48.4 + - + -
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Residues in contact with ILE 113 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88H ILE* 4.5 9.4 - - + -
98H LEU* 3.9 28.5 - - + -
100H ARG* 5.2 6.1 - - + +
109H PHE* 2.9 53.9 + - + +
110H SER* 3.2 18.1 + - - +
112H GLU* 1.3 75.5 - - - +
114H ARG* 1.3 64.5 + - + +
116H TYR* 3.5 1.0 + - - -
117H GLU 3.1 17.0 + - - -
118H LEU* 3.3 28.4 + - + +
119H GLY* 4.2 9.6 - - - +
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Residues in contact with ARG 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110H SER* 3.0 31.4 + - - +
111H GLU* 3.8 20.2 + - - +
113H ILE* 1.3 78.8 - - + +
115H PHE* 1.3 63.8 + - - +
117H GLU* 3.0 20.0 + - - +
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Residues in contact with PHE 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58H LEU* 3.6 27.9 - - + +
68H TYR* 3.4 32.5 - + - -
78H PHE* 3.6 18.8 - + - -
80H ARG* 3.4 55.6 - - - +
111H GLU* 3.0 18.6 + - + +
112H GLU 3.1 3.8 + - - +
114H ARG* 1.3 76.6 - - - +
116H TYR* 1.3 78.4 + + - +
117H GLU* 3.3 8.0 + - - +
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Residues in contact with TYR 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39H ILE* 3.6 22.2 - - - +
57H THR* 3.6 6.2 - - - -
58H LEU* 3.1 24.9 + - + +
59H LEU* 4.3 21.1 - - + -
78H PHE* 4.1 14.1 - + - +
80H ARG* 3.7 17.2 - - - +
81H ASN 5.3 0.9 + - - -
84H SER* 6.0 0.7 - - - -
85H PHE* 3.7 26.4 - + - +
88H ILE* 4.0 20.0 - - + -
92H TYR* 4.6 3.0 + - - +
112H GLU* 2.9 52.3 + - + +
113H ILE 4.3 1.1 - - - +
115H PHE* 1.3 97.3 - + - +
117H GLU* 1.3 68.9 + - - +
118H LEU* 3.4 17.5 + - + +
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Residues in contact with GLU 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56H GLU* 3.7 9.5 - - - +
57H THR* 3.5 16.6 - - - +
58H LEU* 4.0 12.2 + - + +
64H LYS* 2.5 45.3 + - - +
113H ILE 3.1 2.1 + - - -
114H ARG* 3.0 17.2 + - - +
115H PHE 3.7 11.2 - - - +
116H TYR* 1.3 81.3 - - - +
118H LEU* 1.3 64.1 + - - +
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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