Contacts of the helix formed by residues 133 - 148 (chain B) 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 ASP 133 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24B THR* 3.0 34.2 + - + +
25B PHE* 5.3 0.2 - - - -
26B LYS* 5.7 0.3 + - - -
132B PHE* 1.3 72.9 - - - +
134B LYS* 1.3 54.6 + - - +
135B GLU* 3.1 22.8 + - - +
136B GLU* 2.7 45.1 + - + +
137B LEU* 3.2 8.8 + - - +
430B MG 2.4 31.2 - - - -
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Residues in contact with LYS 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ASN* 5.5 5.4 - - - +
117B MET* 3.6 40.8 - - + +
118B ASP* 3.0 31.4 - - - +
121B TYR* 3.6 44.1 - - + -
132B PHE* 3.2 14.9 + - + -
133B ASP* 1.3 70.8 + - - +
135B GLU* 1.3 60.1 + - + +
137B LEU* 3.4 3.3 + - - +
138B LEU* 3.1 28.5 + - - +
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Residues in contact with GLU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ASN* 4.9 12.1 - - - +
133B ASP* 2.9 12.3 + - - +
134B LYS* 1.3 76.9 - - + +
136B GLU* 1.3 68.3 + - + +
138B LEU* 4.0 7.8 - - + +
139B GLU* 3.1 25.5 + - - +
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Residues in contact with GLU 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B THR* 5.5 0.4 - - + -
25B PHE* 3.3 33.2 - - + +
26B LYS* 3.7 26.1 - - + +
27B ALA* 2.7 34.8 + - - +
28B LYS 4.5 0.3 + - - -
133B ASP* 2.7 34.8 + - + +
135B GLU* 1.3 73.7 - - - +
137B LEU* 1.3 63.3 + - - +
139B GLU* 3.6 3.7 + - - +
140B CYS* 3.0 28.9 + - - -
430B MG 4.2 11.1 - - - -
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Residues in contact with LEU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B PHE* 4.1 13.2 - - + -
58B LEU* 5.1 4.7 - - + -
117B MET* 3.7 21.1 - - + -
120B MET* 3.8 22.0 - - + -
132B PHE* 3.7 29.2 - - + -
133B ASP 3.2 4.4 + - - +
134B LYS 3.6 7.6 - - - +
136B GLU* 1.3 75.3 - - - +
138B LEU* 1.3 59.3 + - - +
140B CYS* 3.1 7.4 + - + +
141B ILE* 2.8 47.0 + - + +
164B PRO* 5.2 0.4 - - + -
183B LEU* 4.2 25.1 - - + -
185B VAL* 4.5 10.8 - - + -
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Residues in contact with LEU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LEU* 6.6 0.2 - - + -
110B LEU* 4.2 15.7 - - + -
113B PRO* 3.8 28.9 - - + -
114B ASN* 3.3 36.1 - - - +
117B MET* 3.9 20.3 - - + -
134B LYS 3.1 14.9 + - - +
135B GLU* 4.0 7.4 - - + +
136B GLU 3.4 0.2 - - - -
137B LEU* 1.3 80.0 - - - +
139B GLU* 1.3 56.4 + - - +
141B ILE* 3.3 9.0 + - + +
142B GLN* 2.9 46.8 + - + +
383B ILE* 5.9 2.0 - - + -
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Residues in contact with GLU 139 (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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27B ALA* 3.4 23.8 - - + -
135B GLU 3.1 19.2 + - - +
136B GLU* 3.8 4.9 - - - +
138B LEU* 1.3 74.2 - - - +
140B CYS* 1.3 67.0 + - - +
142B GLN* 3.2 19.2 + - - +
143B GLN* 2.8 48.7 + - + +
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Residues in contact with CYS 140 (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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25B PHE* 4.4 9.4 - - + -
27B ALA* 3.8 24.0 - - - -
30B LEU* 4.1 20.0 - - + -
58B LEU* 4.3 19.8 - - + +
71B PRO* 4.2 16.2 - - - -
73B ILE* 4.4 3.6 - - - +
136B GLU 3.0 21.0 + - - +
137B LEU* 3.1 12.8 + - + +
139B GLU* 1.3 76.0 - - - +
141B ILE* 1.3 63.5 + - - +
143B GLN* 3.1 9.5 + - - +
144B LEU* 2.9 21.8 + - - +
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Residues in contact with ILE 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B LEU* 5.6 1.1 - - + -
98B LEU* 5.0 4.3 - - + -
110B LEU* 5.3 4.3 - - + -
117B MET* 4.1 17.5 - - + -
137B LEU* 2.8 36.5 + - + +
138B LEU* 3.6 13.2 - - + +
140B CYS* 1.3 77.2 - - + +
142B GLN* 1.3 63.4 + - - +
144B LEU* 3.1 9.3 + - + +
145B VAL* 2.8 31.6 + - + +
162B ILE* 4.0 24.5 - - + -
164B PRO* 3.7 30.1 - - + -
185B VAL* 3.9 17.7 - - + -
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Residues in contact with GLN 142 (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 LEU* 4.2 21.5 - - + +
138B LEU* 2.9 42.3 + - + +
139B GLU* 3.2 22.5 + - - +
141B ILE* 1.3 77.5 - - - +
143B GLN* 1.3 53.1 + - - +
145B VAL* 3.2 7.2 + - - +
146B LYS* 2.7 35.8 + - - +
383B ILE* 4.1 14.3 - - - +
384B VAL 4.3 2.6 + - - -
385B LEU 2.8 34.0 + - - +
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Residues in contact with GLN 143 (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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27B ALA* 5.7 0.7 - - + -
30B LEU* 3.7 28.5 - - + -
73B ILE* 4.1 6.4 - - + +
139B GLU* 2.8 38.7 + - + +
140B CYS 3.4 7.0 - - - +
142B GLN* 1.3 74.5 - - - +
144B LEU* 1.3 62.1 + - - +
146B LYS* 3.6 24.7 - - - +
147B LEU* 2.9 29.8 + - - +
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Residues in contact with LEU 144 (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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56B HIS* 3.7 38.6 - - + +
57B MET* 3.7 12.3 - - - +
58B LEU* 3.9 15.3 - - + +
73B ILE* 3.9 18.3 - - + +
140B CYS 2.9 13.3 + - - +
141B ILE* 3.1 10.1 + - + +
143B GLN* 1.3 75.6 - - - +
145B VAL* 1.3 63.7 + - - +
147B LEU* 3.3 4.4 + - - +
148B ASP* 3.1 21.1 + - - +
185B VAL* 3.8 35.7 - - + +
187B LEU* 3.8 24.2 - - + -
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Residues in contact with VAL 145 (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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100B ALA* 4.2 20.0 - - + -
108B ILE* 4.7 9.4 - - + -
110B LEU* 5.3 5.4 - - + -
141B ILE* 2.8 24.6 + - + +
142B GLN* 3.6 7.2 - - - +
144B LEU* 1.3 77.5 - - + +
146B LYS* 1.3 52.0 + - - +
148B ASP 3.1 1.9 + - - -
149B GLN* 2.5 39.7 + - - -
152B VAL* 4.3 14.8 - - + -
160B LEU* 4.6 3.8 - - + -
162B ILE* 3.7 27.8 - - + -
187B LEU* 4.0 20.9 - - + -
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Residues in contact with LYS 146 (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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142B GLN 2.7 21.4 + - - +
143B GLN* 3.6 24.9 - - - +
144B LEU 3.3 0.2 - - - -
145B VAL* 1.3 74.6 - - - +
147B LEU* 1.3 63.5 + - - +
149B GLN* 3.2 37.7 + - - +
385B LEU* 6.3 7.9 - - + -
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Residues in contact with LEU 147 (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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32B VAL* 4.4 15.9 - - + -
34B PRO* 5.4 6.5 - - + -
56B HIS* 3.3 39.2 - - + +
73B ILE* 3.4 29.4 - - + -
143B GLN 2.9 17.3 + - - +
144B LEU* 3.7 4.7 - - - +
146B LYS* 1.3 78.5 - - - +
148B ASP* 1.3 61.6 + - - +
149B GLN* 3.6 3.3 + - - +
150B GLU 5.1 0.3 + - - -
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Residues in contact with ASP 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LEU* 5.8 0.2 - - - +
54B THR* 2.8 24.7 + - - -
55B ASP* 3.8 6.8 - - - +
56B HIS* 2.8 50.2 + - - +
144B LEU 3.1 14.1 + - - +
145B VAL 3.2 2.2 - - - -
147B LEU* 1.3 76.2 - - - +
149B GLN* 1.3 51.1 + - - +
150B GLU* 3.1 3.4 - - - -
151B TRP* 2.7 55.9 + - + +
152B VAL* 4.1 0.8 + - - -
160B LEU* 4.9 1.7 - - - +
187B LEU* 4.0 14.0 - - + +
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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
------------------------------------------------------------
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