Contacts of the helix formed by residues 110 - 124 (chain A) in PDB entry 2CNW
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 GLY 110 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A GLY 3.3 2.2 - - - -
109A SER* 1.3 75.1 - - - +
111A LYS* 1.3 53.8 + - - +
113A THR* 3.6 1.9 + - - -
114A THR* 2.7 39.3 + - - -
217A VAL* 3.9 3.1 - - - -
245A THR* 4.5 0.4 - - - -
1001A GDP 2.8 50.1 + - - -
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Residues in contact with LYS 111 (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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103A LEU* 3.2 23.7 - - + +
104A VAL* 3.4 32.1 - - - -
105A GLY* 3.6 1.6 - - - +
106A LEU 2.8 26.6 + - - -
109A SER* 3.6 2.1 + - - +
110A GLY* 1.3 68.9 - - - +
112A THR* 1.3 64.4 + - - +
114A THR 3.4 0.2 + - - -
115A ALA* 2.9 21.7 + - - +
187A ASP* 3.7 11.1 - - - +
188A THR 3.2 15.7 - - - +
189A ALA 3.8 0.9 - - - -
190A GLY* 3.4 10.5 - - - +
217A VAL* 3.6 26.0 - - + -
1001A GDP 2.6 32.4 + - - +
1007A ALF 2.9 30.4 - - - -
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Residues in contact with THR 112 (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 LYS* 1.3 72.0 - - - +
113A THR* 1.3 64.1 + - - +
115A ALA* 3.3 16.5 + - - +
116A ALA 3.4 4.0 + - - -
141A ALA* 4.9 3.4 + - - +
144A GLN* 3.9 31.7 + - + +
145A LEU* 3.8 24.8 - - + +
148A LEU* 4.1 7.6 - - + +
187A ASP* 2.4 28.1 + - - +
1001A GDP 2.9 14.7 + - - -
1002A MG 2.1 30.4 - - - -
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Residues in contact with THR 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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110A GLY 3.8 3.8 - - - -
112A THR* 1.3 74.6 - - - +
114A THR* 1.3 63.1 + - - +
116A ALA* 3.3 7.3 + - - +
117A LYS* 3.2 37.9 + - + +
144A GLN* 4.6 5.4 + - - -
148A LEU* 4.2 14.7 - - + +
274A GLU 3.7 23.3 - - - +
275A LYS 5.4 1.1 - - - +
1001A GDP 2.7 56.8 + - + +
142D ARG* 5.6 1.0 - - - +
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Residues in contact with THR 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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103A LEU* 3.9 15.0 - - + -
110A GLY 2.7 26.7 + - - -
111A LYS* 3.8 4.3 - - - -
113A THR* 1.3 73.7 - - - +
115A ALA* 1.3 58.9 + - - +
117A LYS* 3.2 14.2 + - - +
118A LEU* 2.9 41.6 + - + +
217A VAL* 4.2 2.8 - - + +
243A VAL* 3.8 27.8 - - + +
245A THR* 3.7 17.8 - - - +
279A LEU* 4.8 8.0 - - + +
1001A GDP 4.9 2.8 + - - -
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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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103A LEU* 3.6 23.3 - - + +
111A LYS 2.9 14.2 + - - +
112A THR 3.3 11.0 + - - +
114A THR* 1.3 74.3 - - - +
116A ALA* 1.3 59.5 + - - +
118A LEU* 3.4 6.4 + - - +
119A ALA* 2.9 28.4 + - - +
131A LEU* 3.5 20.4 - - + +
145A LEU* 4.4 5.4 - - + -
185A LEU* 3.8 5.3 - - + +
187A ASP* 4.4 11.2 - - + -
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Residues in contact with ALA 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 THR 3.4 1.8 + - - +
113A THR 3.3 9.0 + - - +
115A ALA* 1.3 75.5 - - - +
117A LYS* 1.3 60.4 + - - +
119A ALA* 3.3 8.2 + - - +
120A LEU* 2.9 30.8 + - - +
131A LEU* 4.0 6.7 - - + +
145A LEU* 4.6 3.5 - - + +
148A LEU* 3.7 46.0 - - + +
152A VAL* 4.1 10.9 - - + +
276A PRO* 5.0 4.9 - - + -
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Residues in contact with LYS 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 THR* 3.2 28.5 + - + +
114A THR* 3.2 17.3 + - - +
116A ALA* 1.3 77.2 - - - +
118A LEU* 1.3 56.4 + - - +
120A LEU* 3.5 2.8 + - - +
121A TYR* 2.9 28.1 + - - +
271A GLY* 3.7 5.6 - - - -
273A SER 2.8 24.5 + - - -
275A LYS 3.3 18.4 - - - -
276A PRO* 3.6 29.6 - - + +
278A GLY 2.8 29.4 + - - +
279A LEU* 4.0 23.4 - - + +
1001A GDP 3.3 19.6 + - - -
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Residues in contact with LEU 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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101A TRP* 4.3 3.1 - - + -
103A LEU* 4.4 10.3 - - + -
114A THR* 2.9 32.6 + - + +
115A ALA* 3.6 4.7 - - - +
117A LYS* 1.3 72.1 - - - +
119A ALA* 1.3 66.2 + - - +
121A TYR* 3.2 2.4 + - - -
122A TYR* 2.9 42.5 + - + +
185A LEU* 4.1 26.0 - - + -
215A LEU* 4.0 24.2 - - + -
243A VAL* 5.4 0.2 - - + -
269A PHE* 3.6 35.7 - - + -
279A LEU* 3.8 17.5 - - + -
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Residues in contact with ALA 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 ALA 2.9 17.6 + - - +
116A ALA 3.3 5.6 + - - +
118A LEU* 1.3 76.3 - - - +
120A LEU* 1.3 56.2 + - - +
123A LYS* 2.9 31.1 + - - +
129A PRO* 3.3 17.0 - - + +
131A LEU* 4.0 23.6 - - + -
152A VAL* 4.3 2.5 - - + -
154A VAL* 4.1 10.8 - - + -
185A LEU* 3.6 17.9 - - + +
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Residues in contact with LEU 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 ALA 2.9 16.7 + - - +
117A LYS 3.8 3.1 - - - +
119A ALA* 1.3 76.1 - - - +
121A TYR* 1.3 64.0 + - - +
123A LYS* 3.5 13.5 + - + +
124A GLY* 3.2 18.4 + - - -
152A VAL* 3.9 33.3 - - + +
276A PRO* 3.6 32.5 - - + +
277A GLU* 3.9 24.0 - - + +
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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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92A LEU* 3.6 24.9 - - + +
117A LYS 2.9 18.7 + - - +
118A LEU 3.2 4.5 + - - +
120A LEU* 1.3 78.1 - - - +
122A TYR* 1.3 97.3 + + - +
124A GLY* 3.5 8.4 + - - -
125A LYS* 3.5 44.6 + - + +
269A PHE* 4.1 17.9 - + - -
279A LEU* 3.9 24.5 - - + -
281A PRO* 5.4 10.8 - - + +
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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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92A LEU* 5.1 1.6 - - - +
93A PRO* 3.5 18.2 + - - +
95A LEU* 3.6 29.3 - - + +
101A TRP* 3.6 28.4 - + - -
118A LEU* 2.9 36.8 + - + +
119A ALA 4.3 1.1 - - - +
121A TYR* 1.3 99.4 - + - +
123A LYS* 1.3 65.0 + - - +
124A GLY 3.2 1.3 - - - -
125A LYS* 3.0 27.0 + - + +
127A ARG* 2.9 35.3 + - + +
129A PRO* 4.5 0.9 - - + -
183A LEU* 3.3 30.1 - - + -
269A PHE* 3.5 16.2 - + - -
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Residues in contact with LYS 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 ALA 2.9 19.1 + - - +
120A LEU* 3.6 14.0 - - + +
122A TYR* 1.3 75.7 - - - +
124A GLY* 1.3 56.4 + - - +
126A GLY* 3.0 20.3 + - - -
127A ARG 3.6 15.5 - - - +
129A PRO* 3.9 7.7 - - + +
152A VAL 3.3 27.3 + - - +
153A GLY* 3.5 20.0 + - - -
154A VAL* 3.8 12.1 - - + -
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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 LEU 3.2 10.3 + - - -
121A TYR 3.5 4.9 + - - -
122A TYR 3.2 0.8 - - - -
123A LYS* 1.3 78.1 - - - +
125A LYS* 1.3 63.2 + - - +
126A GLY 3.5 1.0 + - - -
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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