Contacts of the helix formed by residues 110 - 124 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B GLY 3.3 3.0 - - - -
109B SER* 1.3 79.3 - - - +
111B LYS* 1.3 54.2 + - - +
113B THR* 3.7 2.1 + - - -
114B THR* 2.6 42.4 + - - -
217B VAL* 4.0 3.8 - - - -
245B THR* 4.4 1.8 - - - -
1001B GDP 3.0 39.7 + - - -
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Residues in contact with LYS 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B LEU* 3.6 13.7 - - + +
104B VAL* 3.5 30.5 - - - +
105B GLY 3.6 1.6 - - - +
106B LEU 2.6 28.4 + - - -
109B SER* 3.5 9.5 + - - +
110B GLY* 1.3 69.7 - - - +
112B THR* 1.3 65.5 + - - +
114B THR* 3.2 2.3 + - - -
115B ALA* 3.0 24.6 + - - +
187B ASP* 3.7 11.7 - - - +
188B THR 3.3 15.7 - - - +
189B ALA 3.9 0.7 - - - -
190B GLY* 3.4 12.5 - - - +
217B VAL* 3.8 22.4 - - + -
1001B GDP 2.6 33.2 + - - +
1007B ALF 2.9 27.4 - - - -
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Residues in contact with THR 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B LYS* 1.3 72.2 - - - +
113B THR* 1.3 64.8 + - - +
115B ALA* 3.4 9.9 + - - +
116B ALA 3.5 7.1 + - - -
141B ALA* 4.8 3.8 + - - +
144B GLN* 3.8 28.0 + - + +
145B LEU* 3.8 28.5 - - + +
148B LEU* 3.9 10.8 - - + +
187B ASP* 2.7 27.3 + - - +
1001B GDP 2.9 15.4 + - - -
1002B MG 2.1 30.3 - - - -
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Residues in contact with THR 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B GLY 3.8 4.5 - - - -
112B THR* 1.3 73.3 - - - +
114B THR* 1.3 61.9 + - - +
115B ALA 3.3 0.2 + - - -
116B ALA* 3.3 7.4 + - - +
117B LYS* 3.2 38.3 + - + +
144B GLN* 4.6 5.0 + - - -
148B LEU* 4.2 13.7 - - + +
274B GLU 3.8 24.0 - - - +
275B LYS 5.6 0.4 - - - -
276B PRO* 6.2 0.2 - - + -
1001B GDP 2.7 64.5 + - + +
142E ARG* 5.3 1.0 - - - +
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Residues in contact with THR 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B LEU* 3.9 14.6 - - + -
110B GLY 2.6 29.7 + - - -
111B LYS* 3.2 5.6 + - - -
113B THR* 1.3 70.3 - - - +
115B ALA* 1.3 54.5 + - - +
117B LYS* 3.1 14.5 + - + +
118B LEU* 2.8 45.3 + - + +
217B VAL* 4.0 2.4 - - + +
243B VAL* 3.7 27.1 - - + +
245B THR* 3.6 18.2 - - - +
279B LEU* 4.8 9.4 - - + -
1001B GDP 4.9 2.1 + - - -
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Residues in contact with ALA 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B LEU* 3.7 26.0 - - + +
111B LYS 3.0 16.4 + - - +
112B THR 3.6 6.3 - - - +
113B THR 3.2 0.4 - - - -
114B THR* 1.3 75.1 - - - +
116B ALA* 1.3 58.9 + - - +
118B LEU* 3.5 6.0 + - - +
119B ALA* 2.9 27.9 + - - +
131B LEU* 3.4 20.1 - - + +
145B LEU* 4.5 1.8 - - + -
185B LEU* 3.8 5.1 - - + +
187B ASP* 4.4 13.5 - - + -
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Residues in contact with ALA 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B THR 3.5 1.8 + - - +
113B THR 3.3 9.5 + - - +
114B THR 3.3 0.2 - - - -
115B ALA* 1.3 77.5 - - - +
117B LYS* 1.3 59.2 + - - +
119B ALA* 3.6 7.7 - - - +
120B LEU* 3.0 28.4 + - - +
131B LEU* 4.0 6.1 - - + +
145B LEU* 4.6 3.1 - - + +
148B LEU* 3.7 46.0 - - + +
152B VAL* 4.0 10.0 - - + +
276B PRO* 4.9 6.1 - - + -
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Residues in contact with LYS 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B THR* 3.2 28.4 + - - +
114B THR* 3.1 16.6 + - - +
116B ALA* 1.3 73.0 - - - +
118B LEU* 1.3 62.4 + - - +
120B LEU* 3.4 1.9 + - - +
121B TYR* 3.0 30.8 + - - +
271B GLY* 4.0 4.4 - - - -
273B SER 2.6 26.3 + - - -
275B LYS 3.3 19.7 - - - -
276B PRO* 3.5 29.2 - - + +
278B GLY 2.9 26.7 + - - +
279B LEU* 4.0 23.0 - - + +
1001B GDP 3.3 18.4 + - - -
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Residues in contact with LEU 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B TRP* 4.2 5.2 - - + -
103B LEU* 3.8 23.8 - - + -
114B THR* 2.8 33.5 + - + +
115B ALA* 3.7 5.2 - - - +
117B LYS* 1.3 73.8 - - - +
119B ALA* 1.3 62.7 + - - +
121B TYR* 4.3 2.5 - - - -
122B TYR* 3.1 41.9 + - + +
185B LEU* 4.0 24.8 - - + +
215B LEU* 4.2 17.3 - - + -
243B VAL* 5.3 0.2 - - + -
269B PHE* 3.6 37.2 - - + -
279B LEU* 3.9 13.2 - - + -
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Residues in contact with ALA 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B ALA 2.9 17.8 + - - +
116B ALA* 3.6 7.4 - - - +
118B LEU* 1.3 77.7 - - - +
120B LEU* 1.3 56.9 + - - +
123B LYS* 3.0 31.8 + - - +
129B PRO* 3.4 8.7 - - + +
131B LEU* 3.9 18.4 - - + -
152B VAL* 4.5 1.8 - - + -
154B VAL* 4.2 19.7 - - + -
185B LEU* 3.7 17.5 - - + +
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Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ALA 3.0 17.4 + - - +
117B LYS 4.0 1.8 - - - +
119B ALA* 1.3 74.1 - - - +
121B TYR* 1.3 66.3 + - - +
123B LYS* 3.5 9.8 + - + +
124B GLY* 3.1 20.3 + - - -
152B VAL* 3.7 33.1 - - + +
276B PRO* 3.5 34.3 - - + +
277B GLU* 3.9 24.2 - - + +
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Residues in contact with TYR 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B LEU* 3.7 25.3 - - + +
117B LYS 3.0 18.7 + - - +
118B LEU 3.8 2.5 - - - +
120B LEU* 1.3 78.8 - - - +
122B TYR* 1.3 96.6 + + - +
124B GLY* 3.4 10.7 + - - -
125B LYS* 3.4 42.7 + - + +
269B PHE* 4.0 19.3 - + - -
279B LEU* 4.0 24.5 - - + -
280B GLU 6.3 0.2 - - - -
281B PRO* 5.1 12.0 - - + +
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Residues in contact with TYR 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B LEU* 5.0 1.9 - - - +
93B PRO* 3.4 30.0 + - - +
95B LEU* 3.6 35.9 - - + +
101B TRP* 3.6 19.1 - + - -
118B LEU* 3.1 30.5 + - + +
119B ALA 4.4 0.9 - - - +
121B TYR* 1.3 104.6 - + - +
123B LYS* 1.3 64.3 + - - +
125B LYS* 3.1 29.3 + - + +
126B GLY 3.3 0.2 + - - -
127B ARG* 3.0 34.2 + - + +
129B PRO* 4.5 0.9 - - + -
183B LEU* 3.5 26.9 - - + -
269B PHE* 3.6 10.9 - + - -
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Residues in contact with LYS 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B ALA 3.0 19.5 + - - +
120B LEU* 3.7 11.9 - - + +
122B TYR* 1.3 75.1 - - - +
124B GLY* 1.3 59.1 - - - +
125B LYS 3.0 0.9 - - - -
126B GLY* 2.9 21.7 + - - -
127B ARG 3.5 13.8 - - - +
129B PRO* 4.0 10.0 - - + +
152B VAL 3.4 24.9 - - - +
153B GLY* 3.0 20.9 + - - -
154B VAL* 4.0 8.9 - - + +
181B ARG* 5.8 3.2 - - - +
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Residues in contact with GLY 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B LEU 3.1 14.5 + - - -
121B TYR 3.4 6.3 + - - -
122B TYR 3.3 0.4 - - - -
123B LYS* 1.3 75.6 - - - +
125B LYS* 1.3 59.7 + - - +
126B GLY 3.7 0.3 + - - -
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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
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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