Contacts of the helix formed by residues 112 - 122 (chain A) in PDB entry 3CPA
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 ASN 112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A GLY 3.5 10.4 + - - +
68A ILE* 3.2 31.4 - - + +
70A SER* 3.8 7.6 + - - -
110A VAL* 3.1 3.5 - - - +
111A THR* 1.3 78.9 - - - +
113A PRO* 1.4 60.2 - - - +
114A ASN* 3.6 5.9 - - - +
115A GLY* 2.9 24.2 - - - +
116A PHE* 3.0 23.6 + - - +
128A LYS 3.1 23.7 - - - +
129A THR* 3.9 24.1 + - + +
175A GLU* 4.6 5.9 + - + -
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Residues in contact with PRO 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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15A LEU* 4.2 9.2 - - + +
19A TYR* 3.5 25.6 - - - +
41A SER* 4.5 5.4 - - - -
45A ARG* 4.0 20.5 - - + -
46A PRO 4.1 7.0 - - - +
47A ILE* 4.3 13.0 - - + -
110A VAL* 3.6 22.2 - - + +
111A THR 3.3 8.5 - - - +
112A ASN* 1.4 87.8 - - - +
114A ASN* 1.3 61.1 + - - +
116A PHE* 3.6 1.6 - - - +
117A ALA* 3.0 28.2 + - - +
175A GLU* 4.4 11.2 - - + -
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Residues in contact with ASN 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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41A SER* 2.6 27.7 + - - -
42A TYR* 3.1 17.3 + - - +
43A GLU* 2.8 36.9 + - - +
45A ARG* 2.8 31.3 + - - +
112A ASN* 3.4 5.5 - - - +
113A PRO* 1.3 72.1 - - - +
115A GLY* 1.4 67.4 - - - +
117A ALA* 3.3 3.5 + - - +
118A PHE* 3.1 22.9 + - - +
130A ARG* 3.9 23.3 - - + +
175A GLU* 3.8 2.2 - - - +
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Residues in contact with GLY 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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70A SER* 3.2 24.0 + - - -
112A ASN* 2.9 19.3 - - - +
114A ASN* 1.4 79.6 - - - +
116A PHE* 1.3 63.2 + - - +
118A PHE* 3.2 4.9 + - - +
119A THR* 3.0 18.9 + - - +
126A TRP* 3.9 8.4 - - - -
128A LYS 3.8 10.8 - - - -
130A ARG* 4.0 3.5 - - - +
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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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13A HIS 3.3 20.2 - - - -
14A THR 3.8 3.4 - - - -
15A LEU* 3.7 45.5 - - + -
18A ILE* 4.0 11.2 - - + -
70A SER* 3.3 5.3 - - - -
73A TRP* 3.7 25.1 - + - -
76A GLN* 3.5 38.8 - - + +
110A VAL* 3.7 15.5 - - + -
112A ASN 3.0 20.0 + - - +
113A PRO 3.6 3.4 - - - +
114A ASN 3.2 0.4 - - - -
115A GLY* 1.3 75.7 - - - +
117A ALA* 1.4 62.5 + - - +
119A THR* 2.7 22.8 + - - -
120A HIS* 3.2 22.6 + + - -
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Residues in contact with ALA 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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15A LEU* 5.0 11.7 - - + -
45A ARG* 3.7 30.7 - - - +
113A PRO 3.0 15.6 + - - +
114A ASN 3.7 4.0 - - - +
116A PHE* 1.4 78.8 - - - +
118A PHE* 1.3 57.3 + - - +
120A HIS* 3.0 11.3 + - - +
121A SER* 2.8 31.4 + - - -
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Residues in contact with PHE 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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114A ASN 3.1 16.6 + - - +
115A GLY* 3.5 5.6 - - - +
116A PHE 3.1 0.6 - - - -
117A ALA* 1.3 75.5 - - - +
119A THR* 1.3 57.6 + - - +
121A SER* 4.3 4.3 - - - +
122A GLU* 2.9 56.9 + - + -
123A ASN* 2.9 33.8 + - + -
126A TRP* 3.5 34.1 - + + -
130A ARG* 3.5 48.5 - - - +
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Residues in contact with THR 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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70A SER 3.9 2.5 - - - -
71A ARG* 3.7 13.0 - - - +
73A TRP* 2.7 34.6 + - - -
115A GLY 3.0 12.7 + - - +
116A PHE* 2.7 22.4 + - - -
118A PHE* 1.3 74.9 - - - +
120A HIS* 1.3 56.5 + - - +
122A GLU 5.2 0.3 - - - -
123A ASN 3.1 12.6 + - - +
124A ARG* 3.2 42.2 + - - +
126A TRP 3.2 25.4 - - - +
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Residues in contact with HIS 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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12A TYR 5.4 0.9 - - - -
13A HIS 3.2 31.8 + - - -
14A THR* 3.8 26.5 - - + +
15A LEU 4.8 1.3 - - - -
73A TRP* 3.3 35.4 - + - -
116A PHE* 3.2 42.1 + + - -
117A ALA* 3.0 10.9 + - - +
119A THR* 1.3 77.4 - - - +
121A SER* 1.3 63.2 + - - +
122A GLU 3.6 0.2 - - - -
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Residues in contact with SER 121 (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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117A ALA 2.8 17.1 + - - -
118A PHE* 4.2 3.8 - - - -
120A HIS* 1.3 81.6 - - - +
122A GLU* 1.3 92.4 + - - +
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Residues in contact with GLU 122 (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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118A PHE* 2.9 40.6 + - + -
119A THR 5.2 0.7 - - - -
120A HIS 3.6 0.4 - - - -
121A SER* 1.3 110.1 + - - +
123A ASN* 1.3 61.5 + - + +
124A ARG 4.1 0.8 + - - -
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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