Contacts of the helix formed by residues 109 - 120 (chain A) in PDB entry 1DXO
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 109 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A ALA* 3.8 22.2 - - + +
42A TYR* 5.8 2.2 - - + +
101A PHE* 3.3 23.3 - - + -
102A PRO* 3.8 14.4 - - + +
104A GLN* 3.9 18.4 - - - +
108A VAL* 1.3 89.4 - - + +
110A ALA* 1.3 66.6 + - - +
111A ILE* 4.1 19.1 - - + -
112A LEU* 2.9 9.8 + - + -
113A LYS 2.9 18.4 + - - -
117C GLU* 3.5 11.0 - - - +
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Residues in contact with ALA 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A PRO* 4.0 2.7 - - - +
108A VAL 3.5 1.6 + - - -
109A PRO* 1.3 71.4 - - - +
111A ILE* 1.3 57.5 + - - +
113A LYS* 4.1 4.0 - - - -
114A GLY* 2.9 26.2 + - - -
48C PRO* 3.9 10.8 - - + +
49C ILE* 5.0 1.6 - - + -
110C ALA* 3.5 18.2 - - + +
113C LYS* 3.9 9.2 - - + -
114C GLY* 3.3 28.0 - - - +
117C GLU* 3.0 25.9 + - - +
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Residues in contact with ILE 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ALA* 4.0 21.8 - - + -
41A LEU* 3.2 54.6 - - + +
42A TYR* 3.8 34.1 - - + +
45A ASN 5.7 0.4 - - - -
46A PHE* 3.9 22.6 - - + +
48A PRO* 4.0 9.0 - - + +
109A PRO* 3.1 8.8 - - + +
110A ALA* 1.3 79.1 - - - +
112A LEU* 1.3 60.9 + - - +
114A GLY 3.8 0.3 + - - -
115A TRP* 3.3 12.0 + - - +
49C ILE* 3.9 25.9 - - + +
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Residues in contact with LEU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A VAL* 4.4 9.9 - - + +
10A ALA* 4.0 19.3 - - + -
41A LEU* 3.7 7.6 - - + -
99A PHE* 4.2 18.2 - - + -
101A PHE* 4.0 26.5 - - + -
108A VAL* 3.9 23.1 - - + -
109A PRO* 2.9 11.7 + - + +
111A ILE* 1.3 80.7 - - - +
113A LYS* 1.3 65.9 + - - +
114A GLY 3.2 0.2 - - - -
115A TRP* 3.0 27.6 + - + -
116A PHE* 3.1 33.3 + - + -
144A LEU* 5.8 0.2 - - + -
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Residues in contact with LYS 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A VAL* 3.6 20.1 - - + +
109A PRO 2.9 12.6 + - - +
110A ALA* 3.6 12.6 - - - +
112A LEU* 1.3 76.0 - - - +
114A GLY* 1.3 58.4 + - - +
116A PHE* 3.1 14.1 + - + +
117A GLU* 3.0 42.0 + - - +
175A ILE* 4.6 5.2 - - + -
104C GLN 2.9 26.6 + - - -
105C TRP* 3.6 23.8 - - - -
107C GLY* 3.7 2.7 - - - -
108C VAL 2.3 43.0 + - - +
110C ALA* 4.1 13.0 - - + +
113C LYS* 5.0 5.2 - - + -
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Residues in contact with GLY 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A PHE* 4.0 5.4 - - - -
48A PRO* 3.0 25.8 - - - -
110A ALA 2.9 12.8 + - - -
113A LYS* 1.3 76.2 - - - +
115A TRP* 1.3 58.8 + - - +
117A GLU* 3.8 4.3 - - - -
118A ARG* 3.1 35.7 + - - +
110C ALA* 3.4 11.4 - - - +
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Residues in contact with TRP 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU* 4.7 8.3 - - + -
8A VAL* 4.0 25.8 - - + -
41A LEU* 3.5 27.1 - - + +
46A PHE* 3.4 28.7 - + + -
87A GLU* 2.7 32.7 + - + -
91A LEU* 4.4 14.6 - - + -
97A VAL* 5.6 0.2 - - + -
99A PHE* 3.6 25.8 - + - -
111A ILE 3.3 14.7 + - - +
112A LEU* 3.0 23.2 + - + +
114A GLY* 1.3 77.6 - - - +
116A PHE* 1.3 68.4 + + - +
119A VAL* 2.8 53.3 + - + +
120A PHE* 3.9 24.9 - + - -
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Residues in contact with PHE 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A PHE* 3.7 37.7 - + - -
108A VAL* 4.5 12.1 - - + -
112A LEU* 3.1 45.6 + - + -
113A LYS* 3.4 14.8 - - + +
115A TRP* 1.3 83.7 - + - +
117A GLU* 1.3 66.7 + - - +
120A PHE* 3.0 46.7 + + + +
144A LEU* 5.8 1.6 - - + -
171A ILE* 5.2 5.6 - - + -
175A ILE* 3.7 41.3 - - + -
176A LEU* 4.6 4.9 - - + -
105C TRP* 3.4 16.8 + - + +
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Residues in contact with GLU 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A PRO 4.4 1.0 - - - +
50A ILE* 3.5 28.3 + - + +
67A TYR* 4.1 1.6 - - - -
113A LYS* 3.0 29.9 + - - +
114A GLY* 3.9 3.4 - - - +
115A TRP 3.4 0.2 - - - -
116A PHE* 1.3 79.2 - - - +
118A ARG* 1.3 59.3 + - - +
120A PHE 4.7 2.9 - - - +
121A ILE* 4.1 11.4 - - - +
104C GLN* 2.7 38.3 + - - +
105C TRP* 3.7 22.4 - - + +
109C PRO* 3.2 13.3 - - - +
110C ALA* 3.0 30.4 + - - +
301C FAD 3.7 15.5 - - + +
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Residues in contact with ARG 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A PHE* 4.2 13.1 - - + -
47A ASN* 2.9 42.2 + - - +
48A PRO 4.0 1.3 - - - +
49A ILE 3.5 17.3 - - - -
50A ILE* 3.4 16.8 - - + +
54A ASP* 2.4 49.1 + - - +
67A TYR* 4.2 4.7 - - - -
81A SER* 4.5 1.6 + - - -
83A ASP* 2.3 36.6 + - - -
84A ILE* 3.4 37.8 - - + +
114A GLY 3.1 18.2 + - - +
115A TRP 4.5 0.4 - - - +
117A GLU* 1.3 79.1 - - - +
119A VAL* 1.3 64.3 + - - +
121A ILE* 3.3 19.7 - - - +
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Residues in contact with VAL 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A PHE* 4.4 6.3 - - + -
84A ILE* 4.5 10.1 - - - +
87A GLU* 3.5 35.7 - - + -
88A GLN* 3.0 30.0 + - + +
91A LEU* 3.7 29.6 - - + -
115A TRP* 2.8 47.7 + - + +
118A ARG* 1.3 77.1 - - + +
120A PHE* 1.3 60.7 + - + +
121A ILE 2.9 8.1 + - - -
124A PHE* 3.3 4.3 - - - -
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Residues in contact with PHE 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A LEU* 3.4 28.5 - - + -
99A PHE* 4.9 3.1 - + - -
115A TRP* 3.9 16.4 - + - -
116A PHE* 3.0 48.6 + + - +
117A GLU 4.7 1.9 - - - +
119A VAL* 1.3 80.3 - - + +
121A ILE* 1.3 66.7 + - - +
122A GLY 3.9 0.7 + - - -
125A ALA* 3.6 17.0 - - + -
126A TYR* 4.0 3.6 - - - -
137A PHE* 4.3 10.3 - + - -
175A ILE* 4.0 14.4 - - + -
176A LEU* 4.7 5.6 - - + -
179A CYS* 3.8 24.9 - - + -
181A PHE* 4.4 13.0 - + - -
105C TRP* 3.4 30.5 + + + -
301C FAD 6.0 0.5 - - - +
302C DQN 4.9 0.9 - - - +
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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