Contacts of the helix formed by residues 112 - 124 (chain A) in PDB entry 3C0M
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 PHE 112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A LEU* 3.5 45.5 - - + +
106A VAL* 4.4 4.9 - - + -
108A ASP* 3.1 11.7 + - + +
110A ALA 3.5 1.4 - - - -
111A ASN* 1.3 81.5 - - - +
113A ILE* 1.3 75.7 + - + +
114A LYS 3.3 0.9 - - - -
115A PRO* 3.1 4.8 - - - +
116A THR* 2.9 54.1 + - + +
151A ILE* 3.7 25.8 - - + -
170A ILE* 5.0 0.7 - - + -
172A VAL* 3.3 29.2 - - + -
314A TYR* 3.6 30.7 - + - -
316A LEU* 4.0 5.2 - - + -
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Residues in contact with ILE 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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106A VAL 3.3 26.9 - - - +
107A HIS* 3.7 21.1 - - - +
108A ASP 2.9 14.9 + - - +
109A SER* 3.8 17.3 - - - -
112A PHE* 1.3 79.1 - - - +
114A LYS* 1.3 60.4 + - + +
116A THR* 3.5 3.2 + - - -
117A SER* 2.7 38.7 + - - +
137A GLY 4.3 13.0 - - - +
140A MET* 4.4 13.0 - - + +
142A VAL* 4.4 12.3 - - + -
151A ILE* 4.2 23.8 - - + -
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Residues in contact with LYS 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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109A SER* 2.7 34.1 + - - +
110A ALA* 4.3 5.2 - - - +
113A ILE* 1.3 75.8 - - - +
115A PRO* 1.3 62.1 - - + +
117A SER* 3.3 4.4 - - - -
118A TYR* 3.0 43.3 + - + -
136A VAL 3.3 24.0 - - - +
137A GLY* 3.2 22.4 - - - +
138A GLU* 3.1 20.3 + - + -
294B LYS* 4.3 0.6 - - - +
296B GLU* 5.6 2.2 + - - -
415B GLU* 2.8 35.8 + - - -
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Residues in contact with PRO 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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110A ALA 3.3 16.4 - - - +
111A ASN* 3.5 21.8 - - - +
112A PHE* 3.1 16.8 - - - +
114A LYS* 1.3 93.4 - - + +
116A THR* 1.3 62.2 + - + +
118A TYR* 3.5 3.3 + - + +
119A LEU* 3.1 18.7 + - - +
388A ASN* 3.1 20.6 + - - +
391A ARG* 3.8 29.6 - - + -
392A VAL* 4.5 8.4 - - - +
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Residues in contact with THR 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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112A PHE* 2.9 61.1 + - + +
113A ILE* 3.5 5.4 + - - -
115A PRO* 1.3 70.2 - - + +
117A SER* 1.3 68.6 + - - +
119A LEU* 3.1 23.0 - - - +
120A ALA* 3.1 9.2 + - - +
151A ILE* 5.3 1.2 - - - +
170A ILE* 4.0 21.0 - - - +
314A TYR* 5.7 0.4 - - - +
316A LEU* 4.0 25.6 - - + -
318A LEU* 4.9 2.4 - - - +
392A VAL* 4.9 12.6 - - + +
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Residues in contact with SER 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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113A ILE* 2.7 24.6 + - - +
114A LYS 3.3 4.5 - - - -
115A PRO 3.2 0.2 - - - -
116A THR* 1.3 81.0 + - - +
118A TYR* 1.3 66.0 + - - +
119A LEU 3.1 0.3 + - - -
120A ALA* 3.1 6.5 + - - +
121A HIS* 2.8 22.3 + - - +
128A VAL* 3.8 16.7 - - - +
136A VAL* 4.6 1.1 - - - -
137A GLY* 3.6 28.3 - - - -
140A MET* 3.8 14.6 - - - +
151A ILE* 5.2 1.2 - - - +
170A ILE* 4.8 7.0 - - - +
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Residues in contact with TYR 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 LYS* 3.0 36.8 + - + +
115A PRO* 3.9 7.2 - - + +
117A SER* 1.3 76.4 - - - +
119A LEU* 1.3 52.3 + - - +
121A HIS* 3.2 9.8 + + - +
122A TYR* 2.7 78.6 + + + -
135A TYR* 5.1 0.2 - - - +
136A VAL* 3.4 40.6 + - + +
388A ASN* 3.9 6.3 - - - +
413B ASN* 6.1 0.7 - - + -
415B GLU* 2.9 50.2 + - + +
416B ILE* 4.5 7.2 + - + -
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Residues in contact with LEU 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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115A PRO 3.1 13.6 + - - +
116A THR* 3.1 11.2 - - - +
117A SER 3.0 0.6 - - - -
118A TYR* 1.3 74.6 - - - +
120A ALA* 1.3 66.2 + - - +
122A TYR* 2.7 16.3 + - + +
123A LEU* 2.8 36.3 + - + +
316A LEU* 4.5 12.6 - - + -
318A LEU* 4.6 5.2 - - + -
343A PHE* 4.4 10.8 - - + -
355A ILE* 3.8 23.8 - - + -
373A TRP* 4.2 8.7 - - + -
385A MET* 5.3 2.5 - - + -
388A ASN* 3.7 12.8 + - - +
389A LEU* 3.7 24.2 - - + -
392A VAL* 4.1 17.3 - - + -
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Residues in contact with ALA 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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116A THR 3.1 7.1 + - - +
117A SER 3.5 7.4 - - - +
119A LEU* 1.3 78.2 - - - +
121A HIS* 1.3 65.6 + - - +
123A LEU* 3.2 1.4 + - - -
124A GLY 3.0 18.5 + - - -
125A TYR* 3.1 30.1 + - + -
128A VAL* 4.3 7.2 - - + -
168A THR* 4.6 0.7 - - + -
170A ILE* 4.0 18.2 - - + -
318A LEU* 3.8 25.5 - - + +
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Residues in contact with HIS 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 SER 2.8 13.8 + - - +
118A TYR* 3.3 19.1 - + - +
120A ALA* 1.3 77.5 - - - +
122A TYR* 1.3 83.5 + + - +
124A GLY 3.2 2.9 + - - -
125A TYR 4.2 2.7 - - - -
128A VAL* 4.3 11.6 + - + +
136A VAL* 4.2 26.2 - - + +
323A ARG* 2.6 62.0 + - - +
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Residues in contact with TYR 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 TYR* 2.7 52.3 + + + +
119A LEU* 2.7 6.2 + - - +
121A HIS* 1.3 88.9 - + - +
123A LEU* 1.3 64.4 + - + +
124A GLY* 3.5 0.3 + - - -
323A ARG* 5.1 0.7 + - - -
375A TRP* 3.8 17.0 - - - -
376A THR* 4.1 7.5 - - - +
380A ASN* 3.3 37.4 - - - +
384A THR* 3.2 28.4 - - + +
385A MET* 4.0 22.2 - - + -
388A ASN* 3.5 33.0 - - + -
281B VAL* 5.5 5.2 - - - +
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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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119A LEU* 2.8 19.3 + - + +
120A ALA 3.5 8.5 - - - +
122A TYR* 1.3 81.1 - - + +
124A GLY* 1.3 58.4 + - - +
125A TYR* 4.3 4.7 - - + -
318A LEU* 4.1 13.7 - - + -
327A ASN* 3.6 2.5 + - - -
328A ALA* 2.7 34.6 + - + +
343A PHE* 3.7 35.0 - - + -
371A TRP* 3.6 39.1 - - + -
373A TRP* 3.8 29.4 - - + -
376A THR* 4.3 11.0 - - + -
385A MET* 5.8 0.7 - - + -
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Residues in contact with GLY 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 ALA 3.0 3.0 + - - -
121A HIS 3.2 3.0 + - - -
122A TYR 4.4 0.2 - - - -
123A LEU* 1.3 80.4 - - - +
125A TYR* 1.3 71.1 + - - +
322A LEU* 4.5 2.5 - - - -
323A ARG* 3.0 46.2 + - - +
326A GLY 4.0 6.5 - - - -
327A ASN* 3.8 13.5 - - - -
375A TRP* 5.4 0.7 - - - -
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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