Contacts of the helix formed by residues 107 - 121 (chain C) in PDB entry 5DSV
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 107 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98C PHE* 3.9 15.9 - - + -
104C TYR* 5.1 5.2 - - + -
105C ASN 3.5 8.3 - - - +
106C ILE* 1.3 89.9 - - + +
108C LEU* 1.3 66.0 + - - +
109C LYS* 4.7 9.0 - - + +
110C HIS* 2.9 25.2 + - + +
111C LEU 3.2 10.2 + - - -
144C ASP* 4.3 20.2 - - - +
102I PHE* 6.2 0.4 - - + -
104I TYR* 3.9 22.7 - - + +
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Residues in contact with LEU 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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73C VAL* 3.7 40.4 - - + -
106C ILE 3.6 4.0 + - - -
107C PRO* 1.3 67.8 - - - +
109C LYS* 1.3 68.5 + - - +
110C HIS 2.9 1.7 + - - -
111C LEU* 4.1 10.5 - - + -
112C ALA* 2.9 24.6 + - - +
137C LEU* 3.5 30.5 - - + +
139C SER* 3.7 22.9 + - - +
147C GLN* 3.4 44.2 - - + +
149C TYR* 3.7 18.6 - - + -
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Residues in contact with LYS 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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107C PRO* 4.6 7.4 - - + +
108C LEU* 1.3 76.2 - - - +
110C HIS* 1.3 59.6 + - + +
112C ALA* 3.7 3.6 - - - +
113C ASP* 3.1 34.9 + - - +
144C ASP* 5.8 2.9 - - - +
147C GLN* 3.6 24.4 - - - +
149C TYR* 3.4 32.6 - - - +
157C SER* 5.0 0.2 + - - -
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Residues in contact with HIS 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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94C GLU* 5.4 1.6 - - + -
98C PHE* 5.0 0.8 - - - -
106C ILE* 3.8 16.5 - - + +
107C PRO* 2.9 20.8 + - + +
108C LEU 2.9 1.0 + - - -
109C LYS* 1.3 77.3 - - + +
111C LEU* 1.3 55.3 + - - +
113C ASP* 2.8 33.8 + - + +
114C ARG* 2.8 49.0 + - + +
101I ASN 3.8 22.3 + - - -
102I PHE* 3.2 55.2 - + - +
104I TYR* 5.8 3.8 - - + +
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Residues in contact with LEU 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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69C VAL* 4.6 9.9 - - + -
73C VAL* 4.1 33.0 - - + -
91C ALA* 3.7 24.9 - - + +
94C GLU* 4.1 12.6 - - + -
95C ALA* 4.0 10.3 - - + -
106C ILE* 3.6 30.0 - - + +
107C PRO 3.2 4.6 + - - +
108C LEU* 3.8 16.6 - - + +
110C HIS* 1.3 80.0 + - - +
112C ALA* 1.3 62.4 + - - +
114C ARG* 3.2 6.2 + - - +
115C VAL* 3.0 33.0 + - + +
137C LEU* 4.2 11.2 - - + -
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Residues in contact with ALA 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 LEU 2.9 21.0 + - - +
109C LYS 3.7 4.0 - - - +
111C LEU* 1.3 72.0 - - - +
113C ASP* 1.3 65.5 + - - +
115C VAL* 3.8 0.6 - - - -
116C ALA* 2.9 25.6 + - - +
137C LEU* 3.9 16.8 - - + +
149C TYR* 3.9 24.0 - - + -
151C ILE* 4.0 7.7 - - + +
157C SER* 3.5 20.0 - - - +
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Residues in contact with ASP 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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109C LYS* 3.1 21.0 + - - +
110C HIS* 2.8 24.7 + - + +
112C ALA* 1.3 74.6 - - - +
114C ARG* 1.3 55.9 + - + +
116C ALA* 3.5 5.6 - - - +
117C MET* 3.1 27.0 + - - +
157C SER* 4.2 13.4 + - - -
85D ARG* 4.7 14.7 + - - -
89D ASP* 5.5 0.2 - - - +
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Residues in contact with ARG 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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94C GLU* 2.7 45.6 + - + +
110C HIS* 2.8 49.4 + - + +
111C LEU* 3.5 6.5 - - - +
112C ALA 3.1 0.2 - - - -
113C ASP* 1.3 70.3 - - - +
115C VAL* 1.3 66.9 + - - +
116C ALA 3.1 1.3 - - - -
117C MET* 3.0 41.2 - - - +
118C TYR* 3.1 6.6 + - - +
101I ASN* 3.5 39.3 + - - +
102I PHE* 5.5 2.6 - - - -
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Residues in contact with VAL 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C LEU* 4.6 17.5 - - + +
90C ILE* 4.4 10.1 - - + +
91C ALA* 3.6 36.6 - - + +
94C GLU* 4.8 2.9 - - + -
111C LEU* 3.0 23.1 + - + +
112C ALA* 4.1 3.4 - - - +
114C ARG* 1.3 81.9 - - + +
116C ALA* 1.3 57.3 + - - +
118C TYR* 3.2 9.4 - - - +
119C VAL* 3.0 29.2 + - + +
135C PHE* 3.5 34.5 - - + -
137C LEU* 5.4 1.6 - - + -
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Residues in contact with ALA 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 ALA 2.9 19.9 + - - +
113C ASP* 3.5 5.6 - - - +
115C VAL* 1.3 72.6 - - - +
117C MET* 1.3 67.3 + - - +
118C TYR 3.0 1.3 - - - -
119C VAL* 2.8 19.1 + - - +
120C HIS* 2.9 13.7 + - - +
151C ILE* 4.0 12.9 - - + +
155C GLY 3.4 21.5 - - - +
157C SER* 3.9 19.1 - - - +
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Residues in contact with MET 117 (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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113C ASP 3.1 10.5 + - - +
114C ARG* 3.0 34.7 + - - +
116C ALA* 1.3 75.6 - - - +
118C TYR* 1.3 58.2 + - - +
120C HIS* 3.4 11.2 + - - +
121C ALA* 3.0 26.9 + - - +
86D SER* 5.6 12.3 - - - +
89D ASP* 3.5 35.7 - - + +
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Residues in contact with TYR 118 (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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87C LEU* 4.4 4.3 - - + -
90C ILE* 3.4 49.7 - - + +
114C ARG 3.1 6.9 + - - +
115C VAL* 3.2 14.8 - - + +
116C ALA 3.0 0.4 - - - -
117C MET* 1.3 78.6 - - + +
119C VAL* 1.3 65.9 + - - +
121C ALA* 3.0 24.6 + - + +
122C TYR* 3.4 31.4 + + - -
131C PHE* 3.9 23.4 - + - -
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Residues in contact with VAL 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C LEU* 3.6 33.7 - - + -
115C VAL* 3.0 17.5 + - + +
116C ALA 2.8 10.6 + - - +
118C TYR* 1.3 71.5 - - - +
120C HIS* 1.3 62.3 + - - +
122C TYR* 3.2 15.8 + - - +
123C THR* 3.7 8.1 - - - +
131C PHE* 4.1 17.9 + - + -
133C CYS 5.5 0.9 - - - +
135C PHE* 4.3 4.9 - - + -
151C ILE* 4.1 14.6 - - + -
152C ASP 3.6 17.0 - - - +
153C PRO* 3.2 26.3 - - + +
155C GLY* 3.7 5.8 - - - -
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Residues in contact with HIS 120 (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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116C ALA 2.9 10.1 + - - +
117C MET* 3.4 13.2 + - - +
119C VAL* 1.3 72.5 - - - +
121C ALA* 1.3 70.0 + - - +
122C TYR 2.9 3.1 + - - -
123C THR* 2.7 39.0 + - - -
124C LEU* 3.9 26.7 - - + +
154C SER 4.1 0.9 - - - -
155C GLY* 3.8 17.4 - - - +
82D ALA* 3.8 21.8 - - + +
83D ASP* 3.0 32.4 + - - -
86D SER* 3.5 32.4 - - - -
131D PHE* 5.0 2.5 - + - -
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Residues in contact with ALA 121 (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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117C MET 3.0 12.7 + - - +
118C TYR* 3.1 18.2 - - + +
120C HIS* 1.3 81.7 - - - +
122C TYR* 1.3 67.2 + - + +
123C THR 3.3 0.9 - - - -
124C LEU* 4.2 6.7 + - - -
125C TYR* 3.4 30.9 - - + -
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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