Contacts of the helix formed by residues 112 - 128 (chain A) in PDB entry 2COJ
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 GLN 112 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A PHE* 1.3 96.8 - - + +
113A PRO* 1.3 71.1 - - - +
114A ASN* 3.2 6.3 - - - +
115A LEU* 3.0 42.3 + - + +
116A ASN* 3.5 5.6 + - - -
289A VAL* 3.6 20.6 - - + -
292A ARG* 5.4 2.4 - - - +
293A CYS* 3.8 5.9 - - - -
296A ASP* 5.4 0.3 - - - +
381A TRP* 2.8 58.6 + - + +
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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
----------------------------------------------------------
98A LEU* 4.3 11.9 - - + -
110A LEU* 3.3 36.1 - - + +
111A PHE* 3.0 7.1 - - - +
112A GLN* 1.3 89.8 - - - +
114A ASN* 1.3 57.1 + - - +
116A ASN* 2.8 35.9 + - - +
117A MET* 3.0 14.9 + - - +
138A LEU* 3.6 28.7 - - + -
381A TRP 4.6 0.9 - - - +
383A ILE* 4.4 18.4 - - + -
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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
----------------------------------------------------------
112A GLN* 3.1 5.1 + - - +
113A PRO* 1.3 77.2 - - - +
115A LEU* 1.3 62.1 + - + +
117A MET* 3.6 9.6 + - - +
118A ASP* 2.8 34.6 + - - +
135A GLU* 3.9 15.3 - - - +
138A LEU* 3.5 21.4 - - - +
383A ILE* 4.1 19.8 - - - +
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Residues in contact with LEU 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A GLN* 3.0 47.0 + - + +
113A PRO 2.9 0.2 + - - -
114A ASN* 1.3 76.9 - - + +
116A ASN* 1.3 64.5 + - - +
118A ASP* 3.0 16.9 + - + +
119A ARG* 2.9 24.2 + - - +
289A VAL* 4.2 22.2 - - + -
292A ARG* 4.5 22.9 - - + -
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Residues in contact with ASN 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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96A GLU* 2.9 31.5 - - + +
97A GLY 3.6 9.7 + - - +
98A LEU* 3.5 31.7 - - + +
111A PHE 4.0 6.1 + - - -
112A GLN 3.5 14.8 + - - -
113A PRO* 2.8 12.8 + - - +
115A LEU* 1.3 77.6 - - - +
117A MET* 1.3 67.9 + - + +
119A ARG* 3.3 13.9 + - - +
120A MET* 2.9 30.5 + - - +
289A VAL* 3.8 15.0 - - - +
333A THR* 5.4 0.2 + - - -
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Residues in contact with MET 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A GLU* 5.4 0.2 - - + -
98A LEU* 5.2 5.6 - - + -
113A PRO 3.0 15.7 + - - +
114A ASN* 3.7 11.2 - - - +
116A ASN* 1.3 88.9 - - + +
118A ASP* 1.3 57.0 + - - +
120A MET* 3.5 13.4 + - - +
121A TYR* 3.0 29.3 + - - +
132A PHE* 4.5 1.8 - - - -
134A LYS* 3.5 41.1 - - + +
137A LEU* 3.8 27.4 - - + -
138A LEU* 4.0 25.6 - - + -
141A ILE* 4.0 20.4 - - + -
164A PRO* 4.8 6.5 - - + -
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Residues in contact with ASP 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ASN* 2.8 26.7 + - - +
115A LEU* 3.0 19.5 + - + +
117A MET* 1.3 77.3 - - - +
119A ARG* 1.3 57.3 + - - +
121A TYR* 3.4 2.6 - - - +
122A ARG* 3.0 28.8 + - - +
134A LYS* 2.5 39.7 + - - +
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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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96A GLU* 2.8 37.6 + - - +
97A GLY 4.7 3.2 + - - -
115A LEU 2.9 15.0 + - - +
116A ASN* 3.6 8.1 + - - +
118A ASP* 1.3 73.8 - - - +
120A MET* 1.3 61.6 + - - +
122A ARG* 3.4 6.7 + - + +
123A SER* 2.9 38.2 + - - +
220A ASP 5.5 4.0 - - - +
221A CYS* 5.7 0.2 - - - -
222A LYS* 3.4 28.4 - - + +
286A LEU* 3.6 14.1 - - - +
287A PRO* 2.9 39.5 + - + -
288A GLY* 3.4 5.1 - - - -
289A VAL* 3.6 11.5 - - - +
410A PLP 2.8 32.5 + - - +
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Residues in contact with MET 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A LEU* 3.7 16.8 - - + +
95A PHE 5.0 0.7 - - - -
96A GLU* 3.6 19.9 + - + -
116A ASN 2.9 18.1 + - - +
117A MET* 3.8 9.4 - - - +
119A ARG* 1.3 75.8 - - - +
121A TYR* 1.3 57.5 + - - +
123A SER* 3.2 7.6 + - - -
124A ALA* 2.8 29.1 + - - +
132A PHE* 3.7 17.5 - - + -
137A LEU* 3.7 26.5 - - + -
164A PRO* 3.7 28.7 - - + -
165A THR 5.2 1.1 - - - +
166A PHE* 4.4 9.6 - - + -
183A LEU* 3.4 33.0 - - + -
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Residues in contact with TYR 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 MET 3.0 18.4 + - - +
118A ASP* 3.4 6.1 - - - +
120A MET* 1.3 72.4 - - - +
122A ARG* 1.3 72.5 + - - +
124A ALA* 3.0 15.5 + - - +
125A VAL* 3.2 26.7 + - + +
131A VAL* 3.6 30.9 - - + +
132A PHE* 3.3 40.1 - + - -
134A LYS* 3.7 28.0 - - + -
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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 ASP 3.0 14.6 + - - +
119A ARG* 3.8 6.7 - - + +
121A TYR* 1.3 86.3 - - + +
123A SER* 1.3 60.8 + - - +
125A VAL* 3.5 7.9 + - - +
126A ARG* 3.1 22.3 + - - +
221A CYS* 4.9 5.7 - - - -
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Residues in contact with SER 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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94A LEU* 3.5 22.4 - - - -
95A PHE 5.5 0.4 + - - -
96A GLU* 5.4 0.2 + - - -
119A ARG* 2.9 20.7 + - - +
120A MET* 3.2 13.1 - - - -
121A TYR 3.0 0.2 + - - -
122A ARG* 1.3 75.3 - - - +
124A ALA* 1.3 65.7 + - - +
126A ARG* 2.9 9.6 + - - +
127A ALA* 2.8 22.7 + - - +
221A CYS* 3.6 14.3 - - - +
222A LYS* 3.5 24.5 + - - +
223A MET* 4.3 3.0 - - - +
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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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94A LEU* 3.2 13.8 - - + +
120A MET 2.8 15.0 + - - +
121A TYR* 3.0 10.7 + - - +
123A SER* 1.3 72.5 - - - +
125A VAL* 1.3 59.3 + - + +
127A ALA* 3.0 1.9 + - - -
128A THR 2.9 8.5 + - - -
129A LEU* 2.8 36.8 + - - +
130A PRO 4.1 5.2 - - - +
131A VAL* 5.1 2.2 - - - -
132A PHE* 4.8 3.6 - - + -
166A PHE* 3.7 30.1 - - + -
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Residues in contact with VAL 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 TYR* 3.2 26.6 + - + +
122A ARG* 3.6 9.2 - - - +
123A SER 3.1 0.2 - - - -
124A ALA* 1.3 76.2 - - - +
126A ARG* 1.3 62.7 + - - +
128A THR* 3.2 12.1 + - - +
129A LEU 4.4 4.0 - - - -
131A VAL* 3.7 27.4 - - + -
232B PHE* 3.2 27.2 - - + -
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Residues in contact with ARG 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 ARG 3.1 14.2 + - - +
123A SER 2.9 8.7 + - - +
125A VAL* 1.3 77.4 - - - +
127A ALA* 1.3 58.8 + - - +
216A GLY 4.2 3.8 + - - -
217A GLY* 3.0 24.9 + - - -
218A THR* 3.5 23.0 - - + +
220A ASP* 4.7 5.9 + - - -
221A CYS* 3.9 23.1 - - - -
223A MET* 4.2 14.5 - - - +
210B TYR* 3.7 29.4 - - - +
228B GLY 5.0 1.6 - - - +
229B SER* 3.8 14.4 + - - +
232B PHE* 3.7 40.1 + - - +
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Residues in contact with ALA 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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92A VAL* 4.6 4.2 - - + +
93A GLU 4.9 4.3 - - - +
94A LEU* 4.2 5.6 - - + -
123A SER 2.8 14.0 + - - +
124A ALA 3.0 4.7 + - - +
126A ARG* 1.3 76.3 - - - +
128A THR* 1.3 79.5 + - - +
129A LEU* 3.5 24.5 + - + +
223A MET* 3.7 24.5 - - + -
228B GLY 4.7 2.3 - - - +
231B LEU* 3.9 13.1 - - - +
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Residues in contact with THR 128 (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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124A ALA 2.9 3.3 + - - -
125A VAL* 3.2 9.3 + - - +
127A ALA* 1.3 90.7 + - - +
129A LEU* 1.3 63.5 + - - +
130A PRO* 4.1 0.3 - - - +
177A LYS* 3.3 40.3 + - - +
178A PRO* 3.6 20.8 - - - +
231B LEU* 3.6 17.4 - - + +
232B PHE* 3.5 41.1 - - + +
235B CYS* 4.1 9.2 - - + -
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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
------------------------------------------------------------
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