Contacts of the helix formed by residues 1427 - 1436 (chain B) in PDB entry 2YIN
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 PRO1427 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1333B MET* 4.3 15.9 - - + -
1425B PRO 3.5 8.5 - - - +
1426B VAL* 1.3 91.9 - - + +
1428B ASP* 1.3 68.0 + - - +
1429B GLN* 4.4 10.5 - - + +
1430B ILE* 2.8 32.8 + - + +
1431B ILE* 3.1 8.8 + - - +
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Residues in contact with ASP1428 (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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1426B VAL 3.6 2.9 + - - +
1427B PRO* 1.3 69.5 - - - +
1429B GLN* 1.3 66.2 + - - +
1431B ILE* 2.8 25.7 + - - +
1432B ASN* 2.8 31.5 + - - +
1511B MET* 3.8 47.8 - - + +
1514B ASN* 4.3 14.9 + - - +
1515B GLN* 5.8 0.3 - - - +
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Residues in contact with GLN1429 (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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1332B ILE* 3.0 22.7 + - - +
1333B MET* 3.4 50.6 - - - +
1335B ILE 5.1 0.6 + - - -
1336B LEU* 3.5 29.9 - - - +
1337B ARG* 5.3 2.3 + - - +
1427B PRO* 4.5 7.0 - - + +
1428B ASP* 1.3 79.2 - - - +
1430B ILE* 1.3 58.6 + - + +
1432B ASN* 4.4 6.8 + - - +
1433B PHE* 4.5 9.5 + - - +
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Residues in contact with ILE1430 (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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1295B GLU* 5.2 2.9 - - - +
1332B ILE* 3.2 32.8 - - + -
1333B MET* 3.5 26.7 - - + -
1421B PHE* 4.4 12.5 - - + -
1426B VAL* 3.4 27.8 - - + -
1427B PRO* 2.8 25.9 + - + +
1429B GLN* 1.3 74.2 - - - +
1431B ILE* 1.3 60.8 + - - +
1432B ASN 3.6 0.2 - - - -
1433B PHE* 4.4 6.6 + - - +
1434B TYR* 3.6 23.0 - - - -
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Residues in contact with ILE1431 (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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1415B LEU* 4.6 23.8 - - + -
1421B PHE* 3.9 36.6 - - + -
1426B VAL* 4.2 15.9 - - + +
1427B PRO 3.1 7.3 + - - +
1428B ASP* 2.8 28.6 + - - +
1430B ILE* 1.3 78.6 - - - +
1432B ASN* 1.3 75.3 + - - +
1433B PHE 3.2 1.8 - - - -
1434B TYR* 3.0 15.1 + - + +
1435B LYS* 3.6 18.3 + - - +
1511B MET* 6.3 0.2 - - + -
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Residues in contact with ASN1432 (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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1428B ASP* 2.8 32.2 + - - +
1429B GLN* 4.6 4.7 - - - +
1431B ILE* 1.3 82.9 - - - +
1433B PHE* 1.3 63.4 + - - +
1435B LYS* 2.5 58.2 + - - +
1436B SER* 3.7 6.6 + - - -
1511B MET* 4.3 17.4 - - - +
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Residues in contact with PHE1433 (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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1292B LYS 4.3 0.2 - - - -
1293B MET* 3.8 25.8 - - + -
1295B GLU* 3.6 36.8 - - + +
1337B ARG* 3.5 45.5 - - + +
1429B GLN 4.5 7.0 + - - +
1430B ILE* 4.4 9.6 - - - +
1431B ILE 3.2 1.2 - - - +
1432B ASN* 1.3 80.1 - - - +
1434B TYR* 1.3 72.6 + + - +
1436B SER* 3.5 1.5 + - - -
1437B ASN* 3.1 60.3 + - + +
1438B TYR* 3.8 18.6 - + - -
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Residues in contact with TYR1434 (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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1295B GLU* 3.9 24.9 - - + +
1415B LEU* 3.7 22.0 - - + +
1416B ASP 4.5 1.7 + - - -
1418B HIS* 3.3 37.1 - + + +
1421B PHE* 3.6 31.9 - + - -
1430B ILE 3.6 19.3 - - - -
1431B ILE* 3.0 12.6 + - + +
1433B PHE* 1.3 88.8 - + - +
1435B LYS* 1.3 63.9 - - - +
1436B SER 3.3 0.4 - - - -
1437B ASN 3.1 14.6 - - - +
1438B TYR* 4.0 37.6 - + + +
1439B VAL* 3.7 7.4 - - - +
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Residues in contact with LYS1435 (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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1413B PRO* 3.3 27.6 - - - +
1414B VAL 4.2 1.4 - - - -
1415B LEU* 4.2 30.1 - - + +
1431B ILE* 3.6 19.3 - - + +
1432B ASN* 2.5 50.1 + - - +
1434B TYR* 1.3 79.9 - - - +
1436B SER* 1.3 60.2 + - - +
1437B ASN 3.7 0.2 - - - -
1439B VAL* 3.5 6.9 - - - +
1511B MET* 4.5 13.1 - - - +
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Residues in contact with SER1436 (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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1339B LYS* 3.5 24.9 - - - +
1340B PRO* 3.6 24.8 - - - +
1342B TYR* 2.6 31.6 + - - -
1413B PRO* 4.1 15.3 - - - +
1432B ASN 3.7 6.6 + - - -
1433B PHE* 3.5 3.4 + - - -
1435B LYS* 1.3 81.7 - - - +
1437B ASN* 1.3 61.8 + - - +
1439B VAL* 4.3 3.1 - - - -
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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