Contacts of the helix formed by residues 114 - 124 (chain A) in PDB entry 3COG
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 TYR 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A LEU* 4.5 2.0 - - + -
113A VAL* 1.3 70.6 - - - +
115A GLY* 1.3 73.0 + - - +
116A GLY* 3.4 29.6 - - - -
117A THR* 2.8 23.5 + - - +
118A ASN* 3.0 9.7 + - - +
157A GLU* 2.7 20.5 + - - +
161A ASN* 3.6 10.0 + - - +
355A THR* 4.5 5.6 - - - -
356A HIS* 3.8 6.1 - + - -
500A PLP 3.3 52.3 - + + +
501A 2AG 1.3 78.6 + - + +
608A NO3 3.3 27.4 - - - -
62B ARG* 3.1 9.3 + - - -
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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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113A VAL 3.2 3.4 + - - -
114A TYR* 1.3 77.3 - - - +
116A GLY* 1.3 55.5 + - - +
118A ASN* 3.3 3.8 + - - +
119A ARG* 2.8 29.6 + - - +
355A THR 3.9 8.3 - - - -
356A HIS* 3.4 8.6 + - - -
358A SER* 3.5 23.3 + - - +
359A VAL* 3.9 19.7 - - - -
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Residues in contact with GLY 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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91A LEU* 3.3 18.6 - - - +
114A TYR* 3.1 25.5 + - - -
115A GLY* 1.3 72.3 - - - +
117A THR* 1.3 59.4 + - - +
119A ARG* 3.7 28.1 + - - +
120A TYR* 3.0 22.5 + - - +
355A THR 4.9 0.4 + - - -
358A SER* 4.2 0.8 + - - -
501A 2AG 5.2 0.6 + - - -
242B SER 4.9 0.3 - - - +
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Residues in contact with THR 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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91A LEU* 4.4 7.0 - - - +
94A THR* 4.6 10.6 + - + -
113A VAL* 4.2 15.0 - - + -
114A TYR* 2.8 26.6 + - - +
116A GLY* 1.3 72.7 - - - +
118A ASN* 1.3 66.6 + - - +
120A TYR* 3.4 4.0 + - - +
121A PHE* 3.1 52.8 + - + -
155A TRP* 3.7 25.2 + - + +
157A GLU* 4.4 2.3 + - - -
187A ASP* 4.7 1.0 + - - -
500A PLP 4.2 9.0 + - - -
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Residues in contact with ASN 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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111A ASP 4.5 10.1 + - - -
113A VAL* 3.8 13.8 + - + +
114A TYR 3.0 9.3 + - - +
115A GLY 3.4 10.3 - - - +
117A THR* 1.3 77.8 - - - +
119A ARG* 1.3 64.4 + - - +
121A PHE* 3.9 1.2 - - - +
122A ARG* 2.9 50.1 + - - +
134A PHE* 3.9 29.8 - - - -
358A SER 4.4 5.8 - - - +
359A VAL* 4.1 32.8 - - + +
363A ASP* 5.0 7.0 + - - +
367A LEU* 5.5 0.8 - - - +
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Residues in contact with ARG 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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91A LEU* 3.6 24.0 - - - +
115A GLY 2.8 20.0 + - - +
116A GLY* 3.7 12.2 + - - +
118A ASN* 1.3 76.2 + - - +
120A TYR* 1.3 58.0 + - - +
122A ARG* 4.8 1.1 - - - +
123A GLN* 2.8 60.9 + - - +
124A VAL* 3.8 1.0 + - + +
358A SER* 3.7 29.3 + - - +
501A 2AG 2.7 42.0 + - - -
62B ARG* 4.0 0.2 - - - +
238B PHE* 4.1 15.5 - - + -
241B ASN* 3.7 19.6 + - - +
242B SER* 3.1 24.4 + - - +
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Residues in contact with TYR 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* 4.8 3.8 - - + -
94A THR* 3.9 14.8 - - + -
95A VAL* 3.7 37.1 + - + +
98A THR* 3.3 41.8 - - + +
99A HIS* 4.2 7.3 - - - -
116A GLY 3.0 18.4 + - - +
117A THR* 3.8 4.3 - - - +
118A ASN 3.3 0.4 - - - -
119A ARG* 1.3 76.8 - - - +
121A PHE* 1.3 79.4 + + - +
124A VAL* 2.9 31.6 + - + -
125A ALA* 2.9 33.1 + - + +
130A LEU* 5.4 0.3 - - - +
99B HIS* 4.8 3.5 + - - -
242B SER* 4.3 11.9 - - - +
243B LEU* 3.7 20.6 - - + -
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Residues in contact with PHE 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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94A THR* 4.0 9.2 - - + -
98A THR* 3.5 22.7 - - - -
107A ILE* 3.9 32.5 - - + -
109A CYS* 3.7 31.9 - - + -
117A THR* 3.1 34.3 + - + +
118A ASN 4.0 1.6 - - - +
120A TYR* 1.3 92.5 - + - +
122A ARG* 1.3 63.5 + - - +
125A ALA* 4.0 4.5 - - + -
126A SER* 3.1 23.9 + - - -
132A ILE* 3.3 29.0 - - + +
134A PHE* 4.4 2.5 - + + -
153A LEU* 4.9 1.6 - - + -
155A TRP* 3.9 29.4 - + + -
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Residues in contact with ARG 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 ASN* 2.9 34.3 + - - +
119A ARG* 4.3 0.9 - - - +
121A PHE* 1.3 77.4 - - - +
123A GLN* 1.3 89.7 + - + +
126A SER* 2.8 23.0 + - - -
132A ILE* 4.9 3.4 - - - -
134A PHE* 4.4 19.9 - - + -
358A SER 4.7 7.1 + - - -
360A LEU* 3.5 48.2 - - - +
363A ASP* 4.5 7.0 - - - -
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Residues in contact with GLN 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 ARG* 2.8 43.0 + - - +
122A ARG* 1.3 108.8 + - - +
124A VAL* 1.3 59.9 + - + +
126A SER* 3.9 2.5 - - - -
127A GLU* 3.6 17.8 - - - +
358A SER* 4.3 7.1 - - - +
238B PHE* 3.6 32.8 - - + -
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Residues in contact with VAL 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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119A ARG 4.5 1.8 - - - +
120A TYR* 2.9 34.3 + - + +
122A ARG 3.8 0.2 - - - -
123A GLN* 1.3 82.2 - - - +
125A ALA* 1.3 66.6 + - - +
126A SER 3.2 1.3 - - - -
127A GLU* 2.9 15.8 + - - +
128A PHE* 3.2 19.2 - - + -
99B HIS* 3.5 33.7 - - + +
238B PHE* 4.0 24.7 - - + -
239B LEU* 4.2 13.9 - - + -
242B SER* 4.5 7.9 - - - -
243B LEU* 4.1 5.4 - - + -
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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