Contacts of the helix formed by residues 241 - 255 (chain S) in PDB entry 1Y1V
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 LEU 241 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1199A ARG* 2.7 39.7 - - - +
1232A ASN* 3.7 32.1 - - - +
1234A GLU* 5.8 3.4 - - + +
240S PRO* 1.3 92.9 - - + +
242S LYS* 1.3 71.1 + - - +
243S GLN 3.0 2.2 - - - -
244S LYS* 2.7 19.6 + - + +
245S ILE* 2.5 41.5 + - + -
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Residues in contact with LYS 242 (chain S).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235S ASP* 2.3 50.5 - - - +
236S LEU* 2.8 29.6 - - - +
240S PRO* 4.2 7.4 - - + -
241S LEU* 1.3 77.9 - - - +
243S GLN* 1.3 52.9 + - + +
245S ILE* 3.5 7.6 - - - +
246S GLU* 2.6 62.0 + - - +
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Residues in contact with GLN 243 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240S PRO* 4.3 13.8 + - + +
241S LEU 2.8 3.2 + - - -
242S LYS* 1.3 73.1 - - + +
244S LYS* 1.3 55.4 + - + +
246S GLU* 3.6 6.5 - - - +
247S GLU* 2.6 56.8 + - - +
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Residues in contact with LYS 244 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1199A ARG* 5.9 4.0 - - - +
240S PRO 4.8 8.1 - - - +
241S LEU* 2.7 25.3 + - + +
243S GLN* 1.3 76.6 - - + +
245S ILE* 1.3 54.1 + - + +
247S GLU* 2.8 14.4 + - - +
248S ILE* 2.6 48.9 + - + +
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Residues in contact with ILE 245 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1199A ARG* 4.1 22.7 - - + +
1203A ASN* 3.9 24.4 + - - +
1231A ASP 4.9 8.7 - - - +
241S LEU* 2.5 45.9 + - + +
242S LYS* 3.7 7.4 - - + +
244S LYS* 1.3 72.5 - - + +
246S GLU* 1.3 60.7 + - + +
248S ILE* 3.7 12.0 + - + +
249S ALA* 3.6 15.8 + - - +
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Residues in contact with GLU 246 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242S LYS* 2.6 49.4 + - - +
243S GLN* 3.7 5.5 + - - +
245S ILE* 1.3 73.2 - - + +
247S GLU* 1.3 66.3 + - + +
249S ALA* 3.3 19.0 + - - +
250S LYS* 3.7 10.0 + - - +
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Residues in contact with GLU 247 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243S GLN* 2.6 41.7 + - - +
244S LYS* 3.3 13.5 - - - +
246S GLU* 1.3 72.9 - - + +
248S ILE* 1.3 65.0 + - + +
250S LYS* 3.1 30.5 + - + +
251S GLN* 3.5 9.2 + - - +
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Residues in contact with ILE 248 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1199A ARG* 4.9 13.2 - - + +
1200A ALA* 3.8 38.1 - - + +
1203A ASN* 3.4 21.5 - - - +
244S LYS* 2.6 31.7 + - + +
245S ILE* 3.9 10.5 - - + +
246S GLU 3.3 0.2 - - - -
247S GLU* 1.3 73.5 - - + +
249S ALA* 1.3 60.3 + - - +
251S GLN* 3.5 19.5 + - - +
252S ASN* 2.9 30.6 + - - +
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Residues in contact with ALA 249 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1132A LYS* 4.8 14.6 - - - +
1203A ASN* 4.6 9.9 - - + -
245S ILE 3.6 8.5 + - - +
246S GLU* 3.3 13.3 + - - +
247S GLU 3.1 1.0 - - - -
248S ILE* 1.3 77.0 - - - +
250S LYS* 1.3 55.0 + - - +
252S ASN* 2.6 35.8 + - - +
253S LEU* 2.9 13.7 + - - +
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Residues in contact with LYS 250 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246S GLU 3.7 8.9 + - - +
247S GLU* 3.1 19.7 + - + +
249S ALA* 1.3 78.4 - - + +
251S GLN* 1.3 64.6 + - - +
253S LEU* 2.8 26.4 + - + +
254S TYR* 3.1 11.8 + - - +
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Residues in contact with GLN 251 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1200A ALA* 5.6 5.4 - - - +
247S GLU 3.5 7.7 + - - +
248S ILE* 3.5 22.7 + - - +
249S ALA 3.3 0.6 - - - -
250S LYS* 1.3 78.0 - - - +
252S ASN* 1.3 61.5 + - - +
254S TYR* 3.2 8.3 - - - +
255S ASN* 3.0 38.1 + - - +
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Residues in contact with ASN 252 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1132A LYS* 6.6 0.4 - - + -
1135A ARG* 3.7 13.3 + - - -
1200A ALA* 3.4 13.5 + - - +
1203A ASN* 3.4 13.9 - - - +
1204A ASP* 2.8 60.2 - - + +
248S ILE* 2.9 21.0 + - - +
249S ALA* 2.6 16.7 + - - +
251S GLN* 1.3 74.5 - - - +
253S LEU* 1.3 66.1 + - - +
254S TYR 3.2 0.2 - - - -
255S ASN* 3.5 13.3 + - - +
256S ALA* 3.6 5.4 + - - +
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Residues in contact with LEU 253 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1128A GLN* 4.5 23.8 - - + +
1132A LYS* 3.4 52.7 - - + +
1284A MET* 4.3 16.6 - - + +
249S ALA 2.9 10.8 + - - +
250S LYS* 2.8 17.1 + - + +
252S ASN* 1.3 74.4 - - + +
254S TYR* 1.3 59.9 - - - +
256S ALA* 2.6 34.9 + - + +
257S GLN* 3.7 14.2 + - - +
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Residues in contact with TYR 254 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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703A THR* 2.9 28.1 - - + +
704A ALA* 4.2 9.9 - - + -
705A LYS* 2.8 58.5 - - - +
706A HIS* 4.3 28.1 + + - -
250S LYS 3.1 7.4 + - - +
251S GLN* 3.2 15.5 - - - +
253S LEU* 1.3 77.0 - - - +
255S ASN* 1.3 62.6 + - - +
256S ALA 2.5 17.3 + - - -
257S GLN* 3.1 22.5 + - - +
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Residues in contact with ASN 255 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1135A ARG* 3.5 13.9 + - - +
1204A ASP* 4.0 15.5 + - - +
1283A VAL* 5.0 2.6 - - - +
251S GLN* 3.0 23.6 + - - +
252S ASN* 3.8 16.8 + - - +
253S LEU 3.2 1.2 - - - -
254S TYR* 1.3 87.8 - - - +
256S ALA* 1.3 57.3 + - - +
257S GLN 3.6 2.1 - - - +
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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