Contacts of the helix formed by residues 109 - 120 (chain A) in PDB entry 1ZX1
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* 4.2 8.7 - - + +
42A TYR* 3.9 17.5 - - - +
101A PHE* 3.8 13.5 - - + -
102A PRO* 3.3 41.5 - - + +
104A TYR* 3.7 28.5 - - + -
108A VAL* 1.3 87.2 - - + +
110A ALA* 1.3 66.1 + - - +
111A ILE* 4.3 9.0 - - + +
112A LEU* 3.0 9.1 + - + +
113A LYS 3.0 18.2 + - - -
117B ASP* 3.9 0.4 - - - +
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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* 3.8 2.7 - - - +
108A VAL 3.5 1.2 + - - -
109A PRO* 1.3 70.8 - - - +
111A ILE* 1.3 57.1 + - - +
113A LYS* 3.5 5.2 - - - +
114A GLY* 2.9 25.8 + - - -
48B PRO* 3.4 23.3 - - + +
110B ALA* 3.5 14.8 - - - +
113B LYS* 3.8 10.3 - - - +
114B GLY* 3.4 31.9 - - - +
117B ASP* 3.0 13.4 + - - +
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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 14.4 - - + -
41A LEU* 3.5 46.3 - - + +
42A TYR* 3.7 50.6 + - + +
46A PHE* 3.7 30.6 - - + +
48A PRO* 4.2 11.3 - - + +
109A PRO* 3.1 3.2 + - + +
110A ALA* 1.3 79.4 - - - +
112A LEU* 1.3 60.8 + - - +
114A GLY* 3.4 2.1 + - - -
115A TRP* 3.1 19.8 + - - +
48B PRO 5.0 1.2 + - - -
49B ARG* 4.1 17.2 - - + +
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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* 3.8 20.9 - - + +
10A ALA* 4.1 17.3 - - + -
41A LEU* 3.8 7.9 - - + -
99A PHE* 3.8 31.6 - - + -
100A GLN 5.2 0.9 - - - +
101A PHE* 3.5 41.1 - - + -
108A VAL* 3.7 21.1 - - + -
109A PRO* 3.0 9.0 + - + +
111A ILE* 1.3 76.2 - - - +
113A LYS* 1.3 66.5 + - - +
114A GLY 3.1 1.6 - - - -
115A TRP* 3.1 7.8 + - + -
116A MET* 3.1 25.5 + - + +
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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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107A SER* 5.5 1.6 - - - +
108A VAL* 3.6 20.2 - - + +
109A PRO 3.0 8.7 + - - +
110A ALA* 3.5 12.6 - - - +
112A LEU* 1.3 76.3 - - - +
114A GLY* 1.3 56.4 + - - +
116A MET* 3.2 22.9 + - + +
117A ASP* 2.7 56.0 + - - +
171A LEU* 6.0 0.4 - - + -
104B TYR* 2.8 27.1 + - - +
105B TRP* 4.2 8.3 - - - -
107B SER* 3.6 18.6 - - - +
108B VAL 2.7 32.4 + - - +
110B ALA* 3.9 14.6 - - + -
113B LYS* 4.5 9.0 - - + -
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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* 3.9 5.2 - - - -
48A PRO* 3.3 29.6 - - - -
110A ALA 2.9 14.0 + - - -
111A ILE 3.8 0.4 - - - -
113A LYS* 1.3 75.2 - - - +
115A TRP* 1.3 59.8 + - - +
117A ASP* 4.2 2.7 - - - -
118A ARG* 2.9 35.9 + - - +
110B ALA* 3.4 8.2 - - - +
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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* 4.4 2.0 - - + -
8A VAL* 3.8 23.8 - - + +
41A LEU* 3.7 32.5 - - + -
46A PHE* 3.3 30.6 - + + -
87A GLU* 2.9 29.0 + - + +
91A VAL* 3.7 31.6 - - + -
97A VAL* 5.1 1.3 - - + -
99A PHE* 3.6 32.1 - + - -
111A ILE 3.1 10.9 + - - +
112A LEU* 3.1 12.2 + - + +
114A GLY* 1.3 75.3 - - - +
116A MET* 1.3 68.7 + - + +
119A VAL* 2.8 49.9 + - + +
120A LEU* 4.2 23.6 - - + -
181A PHE* 6.6 0.2 - + - -
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Residues in contact with MET 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* 5.1 7.4 - - + -
108A VAL* 4.3 21.5 - - - -
112A LEU* 3.1 20.9 + - + +
113A LYS* 3.2 29.8 + - + +
115A TRP* 1.3 95.1 - - + +
117A ASP* 1.3 61.9 + - - +
120A LEU* 3.2 37.6 + - + +
171A LEU* 4.1 18.4 - - + -
175A THR* 3.6 29.8 - - + +
176A LEU* 6.4 0.7 - - + -
105B TRP* 3.2 23.4 + - + +
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Residues in contact with ASP 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 4.8 1.6 - - - +
50A ALA* 4.9 5.7 - - + +
67A TYR* 3.9 9.3 - - - -
113A LYS* 2.7 44.8 + - - +
114A GLY* 3.7 6.1 - - - +
115A TRP 3.4 0.2 - - - -
116A MET* 1.3 73.4 - - - +
118A ARG* 1.3 65.1 + - + +
120A LEU 4.8 4.5 + - - +
121A CYS* 5.5 2.6 - - - +
104B TYR* 3.5 25.8 - - + +
105B TRP* 3.5 17.7 + - - +
110B ALA* 2.9 35.3 + - - +
234B FAD 3.6 18.4 - - + +
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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* 3.4 20.3 - - + -
47A GLU* 2.7 38.7 + - - +
48A PRO 4.2 6.3 - - - +
49A ARG 3.1 19.7 + - - +
50A ALA* 4.3 4.9 - - - -
54A ASP* 2.7 52.4 + - - +
67A TYR* 3.5 15.1 + - - +
71A THR* 5.9 1.2 - - - +
80A LEU* 5.9 0.9 - - - +
81A ALA* 5.0 0.2 - - - +
83A ASP* 2.6 33.3 + - - -
84A ILE* 3.5 37.9 - - + +
114A GLY 2.9 17.8 + - - +
115A TRP 4.4 0.7 - - - +
117A ASP* 1.3 80.5 - - + +
119A VAL* 1.3 64.7 + - - +
121A CYS* 4.5 9.9 - - - +
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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* 4.0 10.1 - - + -
84A ILE* 4.4 8.7 - - - +
87A GLU* 3.6 33.7 - - + +
88A GLN* 2.8 49.0 + - + +
91A VAL* 4.6 4.0 - - + -
115A TRP* 2.8 59.3 + - + +
118A ARG* 1.3 75.0 - - - +
120A LEU* 1.3 65.4 - - + +
121A CYS 3.0 2.3 + - - -
124A PHE* 3.6 4.5 - - + -
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Residues in contact with LEU 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 VAL* 5.2 2.5 - - + -
99A PHE* 6.1 0.9 - - + -
115A TRP* 4.2 21.5 - - + -
116A MET* 3.2 35.8 + - + +
117A ASP 4.8 3.4 - - - +
119A VAL* 1.3 82.7 - - + +
121A CYS* 1.3 60.4 + - - +
124A PHE* 4.5 4.0 - - + -
125A ALA* 3.9 22.0 - - + -
126A PHE* 3.7 3.1 - - - -
137A LEU* 4.3 15.9 - - + -
175A THR* 3.7 29.8 - - + -
176A LEU* 5.7 4.7 - - + -
179A CYS* 4.4 7.0 - - - -
181A PHE* 5.1 5.6 - - + -
105B TRP* 3.3 28.1 + - + -
234B FAD 5.7 1.9 - - - +
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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