Contacts of the helix formed by residues 203 - 220 (chain B) in PDB entry 2LV6
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 ARG 203 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A GLU* 3.4 27.7 + - - -
109A MET* 6.0 0.5 - - - +
124A MET* 4.4 2.2 - - - +
144A MET* 4.9 1.3 - - - -
201B LYS* 2.8 39.2 + - - +
202B ARG* 1.3 101.8 - - - +
204B TRP* 1.3 58.1 + - - +
205B LYS* 2.7 45.4 + - + +
206B LYS* 3.7 26.0 + - + +
207B ASN* 4.2 3.6 + - - +
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Residues in contact with TRP 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A PHE* 3.8 18.5 - + + -
100A ILE* 3.6 24.0 - - + -
105A LEU* 3.0 56.3 - - + -
124A MET* 2.6 42.7 + - + +
125A ILE* 3.3 25.6 - - + -
128A ALA* 3.8 9.2 - - + +
136A VAL* 3.5 20.9 - - + -
141A PHE* 5.0 4.7 - + - -
144A MET* 4.2 17.0 - - + +
145A MET* 2.6 33.0 - - + +
202B ARG 3.1 13.0 + - - -
203B ARG* 1.3 71.4 - - - +
205B LYS* 1.3 50.9 + - - +
207B ASN* 3.5 8.3 - - - +
208B PHE* 2.6 22.8 + - - +
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Residues in contact with LYS 205 (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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11A GLU* 6.0 0.9 - - + -
14A GLU* 5.4 1.6 - - - +
143A THR 4.7 2.0 + - - -
144A MET* 2.6 61.6 + - + +
145A MET* 2.8 17.0 - - - +
147A ALA* 4.8 17.0 - - + +
202B ARG* 5.8 0.2 - - - +
203B ARG* 2.7 35.5 - - + +
204B TRP* 1.3 74.4 - - - +
206B LYS* 1.3 62.8 + - + +
207B ASN 2.9 1.1 - - - -
208B PHE 2.6 2.1 + - - -
209B ILE* 2.5 48.6 + - + +
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Residues in contact with LYS 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLU* 3.1 58.8 - - + +
15A ALA* 4.0 0.7 - - - -
17A SER* 6.0 3.7 - - - -
18A LEU* 3.0 26.5 - - + +
109A MET* 6.2 1.6 - - - +
201B LYS 5.8 7.4 - - - +
203B ARG* 3.7 21.2 + - + +
205B LYS* 1.3 75.0 - - - +
207B ASN* 1.3 57.9 + - - +
209B ILE* 3.5 11.1 - - - +
210B ALA* 2.9 31.0 + - - +
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Residues in contact with ASN 207 (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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18A LEU* 3.2 24.9 - - + +
92A PHE* 4.1 13.4 - - + -
109A MET* 3.0 40.6 - - + +
112A LEU* 2.9 32.0 - - - +
114A GLU* 5.3 2.8 - - - +
203B ARG 4.7 1.8 - - - +
204B TRP* 3.5 15.9 - - - +
205B LYS 2.7 1.0 + - - -
206B LYS* 1.3 81.8 - - - +
208B PHE* 1.3 63.2 + - - +
211B VAL* 3.0 35.7 + - - +
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Residues in contact with PHE 208 (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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84A GLU* 5.1 0.4 - - - -
85A ILE* 2.9 43.5 - - + -
88A ALA* 3.0 36.1 - - + -
92A PHE* 4.5 4.5 - - + -
141A PHE* 3.1 14.1 - + + -
145A MET* 2.5 63.3 - - + -
204B TRP 2.6 8.7 + - - +
205B LYS 2.6 2.6 + - - -
207B ASN* 1.3 69.7 - - - +
209B ILE* 1.3 77.9 + - + -
211B VAL* 2.6 29.4 - - - +
212B SER* 2.6 41.7 + - - -
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Residues in contact with ILE 209 (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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11A GLU* 3.8 44.0 - - + +
12A PHE* 4.7 4.5 - - + -
14A GLU* 5.1 2.7 - - + +
15A ALA* 2.9 27.6 - - + +
72A MET* 4.2 18.8 - - + +
145A MET* 4.5 1.6 - - - +
205B LYS* 2.5 51.3 + - + +
206B LYS* 3.5 7.4 - - - +
208B PHE* 1.3 92.1 - - + +
210B ALA* 1.3 56.5 + - - +
212B SER* 2.6 32.8 + - - -
213B ALA* 2.8 7.6 + - - +
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Residues in contact with ALA 210 (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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15A ALA* 3.2 16.3 - - - +
18A LEU* 2.6 49.8 - - + -
19A PHE* 2.4 43.7 - - + -
206B LYS 2.9 8.2 + - - +
209B ILE* 1.3 79.1 - - - +
211B VAL* 1.3 61.3 + - - +
213B ALA* 2.9 6.7 + - - -
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Residues in contact with VAL 211 (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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18A LEU* 4.3 4.5 - - + -
35A VAL* 3.7 21.1 - - + -
38A SER* 5.0 2.2 - - - +
39A LEU* 3.2 38.1 - - + +
88A ALA* 3.4 28.3 - - + -
91A VAL* 5.5 0.4 - - + -
92A PHE* 5.1 3.6 - - + -
112A LEU* 5.7 2.2 - - + -
207B ASN* 3.0 22.7 - - - +
208B PHE* 2.6 33.5 + - - +
210B ALA* 1.3 75.7 - - - +
212B SER* 1.3 51.3 + - - +
214B ALA* 3.4 0.9 + - - +
215B ASN* 2.7 38.8 + - + +
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Residues in contact with SER 212 (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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72A MET* 5.7 0.4 - - - -
84A GLU* 2.5 63.5 + - - +
208B PHE* 2.6 35.6 + - - -
209B ILE* 2.6 28.6 + - - -
211B VAL* 1.3 73.6 - - - +
213B ALA* 1.3 52.7 + - - -
215B ASN* 4.2 3.6 - - - -
216B ARG 2.8 15.1 + - - -
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Residues in contact with ALA 213 (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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19A PHE* 3.2 22.4 - - + -
68A PHE* 3.4 31.6 - - + -
71A MET* 3.8 15.2 - - + +
72A MET* 4.6 3.1 - - - -
84A GLU* 3.2 7.4 + - - -
209B ILE 2.8 8.6 + - - +
210B ALA 2.9 1.3 + - - +
212B SER* 1.3 79.2 - - - +
214B ALA* 1.3 63.5 + - - +
216B ARG* 3.1 4.3 + - - +
217B PHE* 3.0 21.8 + - - +
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Residues in contact with ALA 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PHE* 3.0 27.7 - - + -
32A LEU* 3.2 26.7 - - + -
35A VAL* 4.2 5.4 - - + -
36A MET* 4.0 17.0 - - + -
39A LEU* 5.0 1.1 - - + -
51A MET* 3.6 5.6 - - - +
210B ALA 3.3 0.2 + - - -
211B VAL 3.9 2.7 - - - +
213B ALA* 1.3 79.5 - - - +
215B ASN* 1.3 66.1 + - - +
217B PHE* 2.8 17.5 + - - +
218B LYS* 3.1 9.8 + - - +
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Residues in contact with ASN 215 (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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36A MET* 6.0 1.3 - - - -
39A LEU* 4.9 10.0 - - + +
41A GLN* 6.4 1.3 - - - -
83A GLU 4.0 0.4 + - - -
84A GLU* 2.4 43.9 - - - +
87A GLU* 2.3 49.2 + - + +
88A ALA* 3.7 2.4 + - - +
211B VAL* 2.7 25.0 + - + +
212B SER 3.9 1.1 - - - +
214B ALA* 1.3 72.9 - - - +
216B ARG* 1.3 61.6 + - - +
218B LYS* 3.1 16.5 + - - +
219B LYS* 3.2 14.1 + - - +
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Residues in contact with ARG 216 (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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71A MET* 4.9 5.8 - - - -
75A LYS* 3.4 33.3 - - + +
78A ASP* 5.3 8.6 + - - -
81A SER* 3.1 39.0 + - - +
82A GLU 3.4 0.8 - - - +
83A GLU* 2.6 43.1 + - - +
84A GLU* 3.4 19.6 - - + +
212B SER 2.8 20.6 + - - +
213B ALA* 3.4 4.7 - - - +
215B ASN* 1.3 78.8 - - - +
217B PHE* 1.3 58.9 + - - +
218B LYS 3.0 0.4 - - - -
219B LYS* 4.3 8.5 - - - +
220B ILE* 2.8 59.2 + - + +
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Residues in contact with PHE 217 (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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32A LEU* 5.5 4.7 - - + -
51A MET* 3.0 56.0 - - + +
54A GLU* 3.3 26.5 - - + -
55A VAL* 3.1 41.7 - - + -
63A ILE* 4.9 5.4 - - + -
71A MET* 4.0 24.7 - - + -
213B ALA 3.0 11.4 + - - +
214B ALA* 2.8 12.3 + - - +
216B ARG* 1.3 78.3 - - - +
218B LYS* 1.3 60.0 + - - +
220B ILE* 3.6 25.6 + - + +
221B SER* 4.6 3.1 + - - -
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Residues in contact with LYS 218 (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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36A MET* 4.0 21.3 - - + +
41A GLN* 2.6 50.4 + - + +
42A ASN 4.7 4.8 - - - +
43A PRO 5.5 1.0 - - - -
47A GLU* 4.7 18.5 + - - +
51A MET* 3.6 5.1 - - - +
87A GLU* 4.9 9.2 - - - +
214B ALA 3.1 8.4 + - - +
215B ASN* 3.4 11.9 - - - +
216B ARG 3.0 0.6 - - - -
217B PHE* 1.3 81.2 - - - +
219B LYS* 1.3 63.5 + - + +
221B SER* 3.1 21.8 + - - -
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Residues in contact with LYS 219 (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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83A GLU* 3.8 32.8 - - + +
87A GLU* 2.7 40.4 - - - +
215B ASN* 3.2 10.3 + - - +
216B ARG* 4.0 9.0 - - - +
218B LYS* 1.3 83.5 - - + +
220B ILE* 1.3 64.7 + - - +
221B SER* 2.7 17.8 + - - +
222B SER* 4.7 1.4 - - - -
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Residues in contact with ILE 220 (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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54A GLU* 5.4 10.1 - - + +
71A MET* 5.1 7.4 - - + -
74A ARG* 6.5 0.9 - - + -
75A LYS* 6.2 0.7 - - + -
78A ASP* 5.5 5.6 - - - +
216B ARG* 2.8 50.3 + - + +
217B PHE* 3.6 44.0 - - + +
218B LYS 3.4 0.4 - - - -
219B LYS* 1.3 76.7 - - - +
221B SER* 1.3 52.1 + - - +
222B SER* 2.5 29.6 + - - -
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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
------------------------------------------------------------
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