Contacts of the helix formed by residues 105 - 127 (chain H) in PDB entry 5VOT
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 SER 105 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63H LEU* 3.6 27.1 - - - +
64H TRP* 3.5 19.1 + - - +
101H VAL 4.9 0.2 - - - -
102H ARG 3.4 9.0 + - - -
103H ALA 2.8 7.7 + - - -
104H SER* 1.3 85.9 + - - +
106H ILE* 1.3 64.8 + - - +
108H PRO* 3.2 19.9 - - - +
109H ILE* 3.1 31.7 + - - +
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Residues in contact with ILE 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100H ALA 4.6 4.7 - - - +
101H VAL* 4.2 17.1 + - - +
103H ALA 4.0 6.0 + - - +
104H SER* 3.2 25.6 - - - +
105H SER* 1.3 74.9 - - - +
107H PHE* 1.3 61.3 + - + +
109H ILE* 3.0 9.4 + - - +
110H LEU* 2.7 57.0 + - + +
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Residues in contact with PHE 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797D TYR* 5.7 10.8 - + + -
101H VAL* 5.5 6.8 + - + -
106H ILE* 1.3 83.6 - - + +
108H PRO* 1.3 63.3 - - + +
110H LEU* 2.9 29.8 + - + +
111H SER* 2.9 24.9 + - - -
148H SER* 4.1 12.4 - - - +
151H ILE* 3.6 33.9 - - + -
152H GLY* 3.6 20.0 - - - +
155H VAL* 4.5 11.9 - - + -
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Residues in contact with PRO 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H VAL* 5.7 8.3 - - + -
63H LEU* 5.1 5.8 - - + -
105H SER* 3.2 36.3 - - - +
106H ILE 3.9 0.2 - - - +
107H PHE* 1.3 94.9 - - + +
109H ILE* 1.3 54.3 + - + +
111H SER* 2.1 31.9 + - - +
112H VAL* 2.9 16.7 + - - +
148H SER 5.2 1.8 - - - +
149H ASN* 5.4 3.6 - - - +
152H GLY* 4.4 13.2 - - - +
155H VAL* 6.4 0.4 - - + -
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Residues in contact with ILE 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H VAL* 6.1 4.7 - - + -
64H TRP* 4.7 12.6 - - + -
104H SER 3.3 26.7 - - - +
105H SER* 3.1 16.2 + - - +
106H ILE* 3.0 10.6 + - - +
108H PRO* 1.3 73.0 - - + +
110H LEU* 1.3 68.5 + - + +
112H VAL* 2.9 23.8 + - + +
113H ILE* 2.9 30.7 + - + +
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Residues in contact with LEU 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106H ILE* 2.7 33.5 + - + +
107H PHE* 2.9 42.8 + - + +
109H ILE* 1.3 74.6 - - + +
111H SER* 1.3 54.5 + - - +
113H ILE* 3.4 15.2 + - + +
114H LEU* 2.9 42.6 + - + +
148H SER* 4.6 9.4 - - - -
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Residues in contact with SER 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H MET* 5.3 4.7 - - - +
107H PHE 2.9 10.1 + - - -
108H PRO* 2.1 32.1 + - - +
110H LEU* 1.3 76.5 - - - +
112H VAL* 1.3 57.2 + - - +
114H LEU* 4.0 2.4 - - - +
115H LEU* 2.9 44.8 + - - +
145H ALA* 4.1 3.4 - - - -
148H SER* 3.4 22.2 + - - -
149H ASN* 4.0 23.8 - - - +
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Residues in contact with VAL 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H PHE* 4.3 14.2 - - + -
24H MET* 5.2 10.1 - - + -
25H THR* 5.8 5.2 - - - +
28H VAL* 4.5 20.6 - - + -
108H PRO 2.9 20.4 + - - +
109H ILE* 2.9 20.7 + - + +
111H SER* 1.3 77.8 - - - +
113H ILE* 1.3 68.4 + - + +
115H LEU* 3.7 7.1 - - - +
116H PHE* 2.9 23.7 + - + +
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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
----------------------------------------------------------
109H ILE* 2.9 33.8 + - + +
110H LEU* 3.9 15.9 - - + +
112H VAL* 1.3 77.6 - - + +
114H LEU* 1.3 62.5 + - + +
116H PHE* 3.1 13.4 + - + +
117H MET* 2.9 36.6 + - + +
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Residues in contact with LEU 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110H LEU* 2.9 26.5 + - + +
111H SER 4.0 0.7 - - - +
113H ILE* 1.3 80.8 - - + +
115H LEU* 1.3 57.4 + - - +
117H MET* 3.2 13.6 + - + +
118H GLY* 2.9 22.2 + - - -
141H PHE* 4.1 26.0 - - + +
142H PHE* 5.3 0.7 - - - -
144H SER* 4.6 4.0 - - - +
145H ALA* 3.4 38.7 - - + +
148H SER* 3.8 14.4 - - - +
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Residues in contact with LEU 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H ALA 6.2 0.2 - - - +
20H ALA* 4.0 27.1 - - + +
21H PHE* 4.0 22.2 - - + +
24H MET* 4.1 15.9 - - + -
111H SER* 2.9 33.1 + - - +
112H VAL* 3.7 4.3 - - - +
114H LEU* 1.3 71.9 - - - +
116H PHE* 1.3 59.2 + - - +
118H GLY* 2.6 22.0 + - - +
119H GLY* 2.9 12.6 + - - -
142H PHE* 3.6 32.7 - - + +
145H ALA* 4.5 11.0 - - + -
146H GLY* 5.6 1.8 - - - +
190H ALA* 4.7 11.4 - - + -
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Residues in contact with PHE 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H PHE* 4.0 27.0 - + + -
112H VAL* 2.9 14.7 + - + +
113H ILE* 3.2 16.4 - - + +
115H LEU* 1.3 75.7 - - - +
117H MET* 1.3 68.6 + - - +
119H GLY* 4.2 0.4 - - - -
120H LEU* 2.9 44.0 + - + +
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Residues in contact with MET 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113H ILE* 2.9 26.8 + - + +
114H LEU* 3.4 15.9 - - + +
115H LEU 3.2 0.2 - - - -
116H PHE* 1.3 88.9 - - + +
118H GLY* 1.3 56.8 + - - +
120H LEU* 4.3 6.1 - - + -
121H CYS* 2.9 59.1 + - - +
138H ALA* 4.8 0.9 - - - +
141H PHE* 5.6 15.0 - - + -
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Residues in contact with GLY 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H LEU 2.9 10.3 + - - -
115H LEU* 2.6 17.1 + - - -
117H MET* 1.3 72.4 - - - +
119H GLY* 1.3 61.8 + - - -
121H CYS* 3.8 1.3 - - - +
122H ILE* 2.9 35.6 + - - +
138H ALA* 5.0 5.6 - - - -
141H PHE* 6.3 1.3 - - - +
142H PHE* 4.6 22.4 - - - -
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Residues in contact with GLY 119 (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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17H ALA* 4.4 22.6 - - - +
115H LEU 2.9 12.7 + - - -
116H PHE* 4.2 0.4 - - - -
118H GLY* 1.3 71.6 - - - -
120H LEU* 1.3 56.9 + - - +
122H ILE* 3.9 5.5 - - - +
123H ALA* 2.9 33.3 + - - +
142H PHE* 6.0 0.8 - - - -
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Residues in contact with LEU 120 (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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116H PHE* 2.9 36.4 + - + +
117H MET* 4.1 8.1 - - - +
119H GLY* 1.3 77.8 - - - +
121H CYS* 1.3 58.7 + - - +
123H ALA* 3.6 5.1 + - - +
124H ALA* 2.9 26.7 + - - +
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Residues in contact with CYS 121 (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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117H MET* 2.9 53.3 + - - +
120H LEU* 1.3 76.5 - - - +
122H ILE* 1.3 61.0 + - - +
124H ALA* 3.3 10.6 - - + +
125H SER* 2.9 23.6 + - - -
134H ILE* 3.7 11.4 - - + +
137H SER* 5.6 2.0 - - - +
138H ALA* 3.7 21.1 - - + -
141H PHE* 6.3 3.6 - - - -
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Residues in contact with ILE 122 (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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10H MET* 6.1 4.9 - - + -
13H THR* 3.5 38.6 - - + +
14H THR* 5.8 4.7 - - + -
17H ALA* 5.5 4.7 - - + -
118H GLY* 2.9 28.5 + - - +
119H GLY* 3.9 6.1 - - - +
121H CYS* 1.3 74.3 - - - +
123H ALA* 1.3 59.3 + - - +
124H ALA 3.0 1.1 - - - -
125H SER* 2.3 42.4 + - - +
126H GLU* 3.0 5.9 + - - +
135H ILE* 6.5 0.2 - - - -
138H ALA* 4.2 15.7 - - + +
142H PHE* 5.5 14.8 - - + -
197H ALA* 6.0 5.4 - - + -
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Residues in contact with ALA 123 (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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119H GLY 2.9 17.7 + - - +
120H LEU* 3.9 5.4 - - - +
122H ILE* 1.3 75.9 - - - +
124H ALA* 1.3 60.2 + - - +
126H GLU* 3.2 28.5 - - - +
127H PHE* 4.0 9.0 - - - -
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Residues in contact with ALA 124 (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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120H LEU 2.9 16.0 + - - +
121H CYS* 3.3 15.9 - - - +
122H ILE 3.0 0.2 - - - -
123H ALA* 1.3 76.3 - - - +
125H SER* 1.3 56.9 + - - +
126H GLU 3.1 2.0 + - - -
127H PHE* 2.9 34.8 + - - +
128H TYR* 4.7 4.7 - - - +
134H ILE* 5.0 5.2 - - + -
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Residues in contact with SER 125 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H MET* 6.2 0.2 - - - -
121H CYS 2.9 12.4 + - - -
122H ILE* 2.3 43.3 + - - +
124H ALA* 1.3 69.6 - - - +
126H GLU* 1.3 64.4 + - - +
127H PHE 3.4 5.1 - - - +
128H TYR 5.7 0.7 - - - -
129H LYS* 5.0 8.3 - - - +
130H THR* 6.0 0.4 - - - -
134H ILE* 3.8 21.3 - - - -
135H ILE* 4.9 12.8 - - - -
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Residues in contact with GLU 126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H MET* 6.3 4.0 - - - -
122H ILE 3.0 6.7 + - - +
123H ALA* 3.2 24.0 - - - +
124H ALA 3.1 0.6 - - - -
125H SER* 1.3 79.7 + - - +
127H PHE* 1.3 71.3 + - + +
129H LYS* 5.8 1.0 - - - -
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Residues in contact with PHE 127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123H ALA 4.0 15.0 - - - -
124H ALA* 2.9 25.5 + - - +
125H SER* 3.7 4.9 - - - +
126H GLU* 1.3 92.9 - - + +
128H TYR* 1.3 86.5 + - + +
129H LYS* 3.5 3.1 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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