Contacts of the helix formed by residues 111 - 127 (chain A) in PDB entry 1CEZ
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 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A ILE* 4.2 5.4 - - + +
85A ILE* 3.6 22.8 - - + +
86A ASN* 3.6 31.6 - - - +
89A PHE* 5.3 6.3 - - + -
109A ILE 3.3 9.4 - - - +
110A LYS* 1.3 86.4 - - + +
112A GLU* 1.3 73.1 + - - +
114A VAL* 4.3 8.5 - - + -
115A ALA* 2.9 31.2 + - - +
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Residues in contact with GLU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A GLU* 4.3 22.9 - - + +
46A MET 5.3 0.3 + - - -
78A LEU* 4.4 4.1 - - + +
82A ILE* 3.7 40.8 - - + +
86A ASN* 4.8 1.2 - - - +
110A LYS* 3.0 36.2 + - + +
111A PRO* 1.3 88.0 - - - +
113A ALA* 1.3 60.6 + - - +
115A ALA* 4.1 1.7 - - - +
116A TYR* 3.2 24.1 + - - +
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Residues in contact with ALA 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A TYR 3.3 21.0 - - - +
45A GLU* 4.4 5.1 - - - +
109A ILE* 4.2 1.6 - - + -
110A LYS* 2.9 18.8 + - + +
112A GLU* 1.3 78.4 - - - +
114A VAL* 1.3 66.8 + - - +
116A TYR 3.3 0.2 + - - -
117A ILE* 2.9 31.8 + - + +
148A GLU* 3.9 28.9 - - + +
155A ARG* 4.5 4.7 - - - +
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Residues in contact with VAL 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A MET* 5.3 0.4 - - + -
85A ILE* 3.7 23.6 - - + -
89A PHE* 6.0 0.7 - - + -
106A LEU* 4.1 21.3 - - + +
109A ILE* 3.6 28.7 - - + +
110A LYS 3.1 13.9 + - - +
111A PRO* 3.2 9.4 + - + +
113A ALA* 1.3 77.2 - - - +
115A ALA* 1.3 61.7 + - - +
117A ILE* 4.0 1.2 - - - +
118A THR* 2.8 31.0 + - - +
145A ILE* 4.0 10.9 - - + +
216A CYS* 3.9 27.6 - - - -
219A MET* 5.2 2.5 - - + -
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Residues in contact with ALA 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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78A LEU* 3.7 8.7 - - + -
81A MET* 3.3 32.0 - - + +
82A ILE* 3.7 22.9 - - + -
85A ILE* 3.6 5.6 - - + +
111A PRO 2.9 16.5 + - - +
112A GLU 4.1 0.4 - - - +
114A VAL* 1.3 78.5 - - - +
116A TYR* 1.3 61.0 + - - +
118A THR* 3.6 1.9 - - - -
119A ILE* 3.0 32.7 + - - +
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Residues in contact with TYR 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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42A GLU* 3.1 34.0 + - - +
43A SER 5.3 0.4 - - - -
44A TYR 4.2 4.5 - - - +
45A GLU* 3.5 9.0 - - - -
46A MET* 3.3 51.2 - - + +
74A ILE* 4.0 25.8 - - + -
78A LEU* 4.0 9.6 - - + +
112A GLU 3.2 17.3 + - - +
113A ALA 3.9 2.7 - - - +
115A ALA* 1.3 79.9 - - - +
117A ILE* 1.3 63.0 + - - +
119A ILE* 3.5 1.6 + - - +
120A LYS* 3.1 52.5 + - + +
263A GLY 2.8 28.5 + - - -
264A ILE* 4.3 0.7 - - - -
265A SER* 4.5 1.9 + - - -
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Residues in contact with ILE 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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43A SER 4.0 13.5 - - - +
44A TYR* 3.7 23.6 - - + +
109A ILE* 5.9 0.2 - - + -
113A ALA 2.9 23.8 + - - +
114A VAL 4.0 2.7 - - - +
116A TYR* 1.3 76.6 - - - +
118A THR* 1.3 58.8 + - - +
120A LYS* 4.1 3.1 - - - +
121A THR* 2.5 41.9 + - - +
141A ILE* 4.4 3.4 - - + +
144A ALA* 3.4 38.6 - - + +
145A ILE* 4.0 22.4 - - + -
148A GLU* 3.9 26.9 - - + -
267A MET* 5.1 4.0 - - + -
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Residues in contact with THR 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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81A MET* 3.4 25.1 - - + +
114A VAL* 2.8 21.9 + - - +
115A ALA 3.6 4.5 - - - -
117A ILE* 1.3 75.5 - - - +
119A ILE* 1.3 65.7 + - - +
121A THR* 4.2 0.3 - - - -
122A THR* 2.8 34.9 + - - +
141A ILE* 4.3 14.6 - - + +
145A ILE* 4.8 0.5 - - - +
216A CYS* 3.5 39.3 - - + +
217A ILE 4.6 0.2 - - - +
220A LEU* 4.1 16.8 - - + -
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Residues in contact with ILE 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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74A ILE* 4.0 29.6 - - + -
77A LEU* 4.2 25.4 - - + +
78A LEU* 5.1 4.3 - - - +
81A MET* 4.5 14.8 - - + -
115A ALA 3.0 24.6 + - - +
116A TYR* 3.7 5.4 - - - +
118A THR* 1.3 79.7 - - - +
120A LYS* 1.3 62.8 + - + +
122A THR* 3.8 2.6 - - - -
123A LEU* 3.1 30.8 + - + +
220A LEU* 3.6 27.8 - - + -
226A MET* 4.2 5.2 - - - +
264A ILE* 4.0 17.3 - - + -
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Residues in contact with LYS 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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42A GLU* 3.5 21.7 + - - -
43A SER* 4.2 1.0 + - - +
116A TYR* 3.1 53.4 + - + +
117A ILE* 5.5 0.6 - - - +
119A ILE* 1.3 77.7 - - + +
121A THR* 1.3 65.7 + - - +
123A LEU* 3.6 2.0 + - - +
124A ALA* 3.1 24.3 + - - +
264A ILE* 3.6 27.4 - - + -
265A SER* 2.9 30.1 + - - +
266A PRO* 4.3 2.5 - - - +
267A MET* 2.9 56.6 - - + +
400A PHE* 4.8 2.9 - - - -
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Residues in contact with THR 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ILE* 2.5 35.9 + - - +
120A LYS* 1.3 72.7 - - - +
122A THR* 1.3 64.6 + - - +
124A ALA* 3.3 5.7 + - + +
125A CYS* 3.0 26.0 + - - -
140A ALA* 3.6 44.6 - - + +
141A ILE* 3.8 15.3 - - + -
144A ALA* 4.2 3.6 - - + +
267A MET* 3.4 17.7 - - + +
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Residues in contact with THR 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A THR* 2.8 22.6 + - - +
119A ILE 3.8 2.7 - - - -
121A THR* 1.3 78.4 - - - +
123A LEU* 1.3 62.2 + - - +
125A CYS* 3.4 3.0 + - - +
126A LEU* 3.2 24.5 + - + +
137A VAL* 4.1 15.4 - - + +
141A ILE* 3.6 18.5 - - - +
217A ILE* 4.7 3.1 - - + +
220A LEU* 3.9 15.6 - - + +
226A MET* 3.9 8.5 - - + -
227A VAL* 3.9 29.2 - - + -
244A ILE* 4.6 8.7 - - + -
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Residues in contact with LEU 123 (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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73A LEU* 6.4 1.1 - - + -
77A LEU* 5.3 1.1 - - + -
119A ILE* 3.1 26.6 + - + +
120A LYS 4.1 1.8 - - - +
121A THR 3.4 0.2 - - - -
122A THR* 1.3 77.3 - - - +
124A ALA* 1.3 62.0 + - - +
126A LEU* 3.3 20.1 + - + +
127A THR* 3.5 13.3 - - - +
226A MET* 3.8 23.6 - - + -
246A LEU* 4.5 11.2 - - + -
254A ILE* 4.3 23.8 - - + -
261A LEU* 4.9 9.4 - - + -
264A ILE* 4.0 34.8 - - + -
396A ILE* 3.7 16.7 - - + +
400A PHE* 3.8 16.2 - - + -
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Residues in contact with ALA 124 (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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120A LYS 3.1 18.7 + - - +
121A THR* 3.5 7.6 - - + +
122A THR 3.2 0.2 - - - -
123A LEU* 1.3 76.4 - - - +
125A CYS* 1.3 64.3 + - - +
127A THR* 2.8 33.5 + - - -
128A SER* 5.5 0.2 - - - -
266A PRO* 5.9 1.3 - - + -
267A MET* 5.7 8.7 - - + +
400A PHE* 4.0 6.4 - - + -
431A MET* 4.0 19.3 - - + +
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Residues in contact with CYS 125 (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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121A THR* 3.0 23.4 + - - +
122A THR 3.4 4.9 + - - +
124A ALA* 1.3 76.3 - - - +
126A LEU* 1.3 57.1 + - - +
127A THR 3.1 0.2 - - - -
128A SER* 3.1 29.0 + - - -
131A ASN 4.4 3.3 - - - +
132A THR* 3.6 7.7 - - + +
136A ALA* 4.3 3.8 - - + -
137A VAL* 3.9 35.0 - - + -
140A ALA* 3.6 30.1 - - - -
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Residues in contact with LEU 126 (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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122A THR* 3.2 20.2 + - + +
123A LEU* 3.5 18.2 - - + +
124A ALA 3.1 0.6 - - - -
125A CYS* 1.3 72.9 - - + +
127A THR* 1.3 55.0 + - - +
128A SER 2.9 9.1 + - - +
132A THR* 4.2 15.0 - - + +
227A VAL* 3.9 24.5 - - + -
244A ILE* 3.7 30.7 - - + +
245A GLU* 4.7 0.4 - - - +
246A LEU* 3.9 33.9 - - + +
389A LYS* 6.2 0.9 - - - -
393A SER* 3.0 27.1 - - - -
396A ILE* 5.0 10.3 - - + -
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Residues in contact with THR 127 (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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123A LEU 3.5 12.3 - - - +
124A ALA* 2.8 21.5 + - - +
126A LEU* 1.3 76.6 - - - +
128A SER* 1.3 59.2 + - - +
129A ALA 3.8 1.4 + - - -
393A SER* 4.0 15.6 - - - +
394A ARG* 5.8 0.2 - - - -
396A ILE* 3.8 8.7 - - + -
397A SER* 4.0 22.8 - - - -
400A PHE* 3.7 27.4 - - + -
431A MET* 4.4 12.1 - - + +
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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
------------------------------------------------------------
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