Contacts of the helix formed by residues 1252 - 1261 (chain A) in PDB entry 1YW2
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 SER1252 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1195A LEU 4.7 3.4 + - - -
1196A ASN* 6.1 1.1 - - - -
1197A TRP* 3.8 17.4 - - - +
1250A ILE* 3.4 0.4 - - - +
1251A SER* 1.3 80.4 + - - +
1253A GLU* 1.3 51.8 + - - +
1254A SER* 3.8 3.8 + - - -
1255A ALA* 2.7 35.9 + - - +
1256A ARG* 2.8 33.8 + - - +
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Residues in contact with GLU1253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1251A SER 2.8 6.9 + - - -
1252A SER* 1.3 69.2 - - - +
1254A SER* 1.3 68.2 + - - +
1256A ARG* 3.0 33.6 + - - +
1257A ASN* 2.9 47.4 + - - +
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Residues in contact with SER1254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1252A SER* 3.4 3.7 + - - -
1253A GLU* 1.3 82.9 - - - +
1255A ALA* 1.3 62.7 + - - +
1257A ASN* 3.3 5.4 + - - +
1258A TYR* 2.8 55.4 + - - -
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Residues in contact with ALA1255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1195A LEU* 4.1 18.4 - - + +
1197A TRP* 3.4 30.1 - - + +
1250A ILE* 4.0 0.7 - - + -
1252A SER* 2.7 35.0 + - - +
1254A SER* 1.3 73.1 - - - +
1256A ARG* 1.3 64.8 + - - +
1257A ASN 3.2 0.2 + - - -
1258A TYR* 3.4 4.4 + - - +
1259A ILE* 2.8 29.1 + - - +
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Residues in contact with ARG1256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1247A LEU* 4.5 9.9 - - + +
1248A LYS* 6.5 0.4 - - - +
1250A ILE* 2.8 51.2 + - + +
1251A SER* 2.5 29.9 + - - +
1252A SER 2.8 16.5 + - - +
1253A GLU* 3.0 41.3 + - - +
1255A ALA* 1.3 74.9 - - - +
1257A ASN* 1.3 62.9 + - - +
1259A ILE* 3.4 5.2 + - - +
1260A GLN* 2.7 46.5 + - + +
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Residues in contact with ASN1257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1253A GLU* 2.9 45.3 + - - +
1254A SER* 3.9 6.3 - - - +
1256A ARG* 1.3 82.4 - - - +
1258A TYR* 1.3 54.2 + - + +
1260A GLN* 2.9 9.1 + - - +
1261A SER* 2.6 42.5 + - - -
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Residues in contact with TYR1258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1195A LEU* 5.4 6.7 - - + -
1229A ILE* 5.2 15.9 - - + -
1232A LEU* 5.8 6.4 - - + +
1236A LEU* 5.6 0.2 - - - +
1254A SER* 2.8 47.3 + - - +
1255A ALA* 3.4 6.0 + - - +
1257A ASN* 1.3 77.9 - - + +
1259A ILE* 1.3 60.8 + - + +
1261A SER* 2.7 30.5 + - - +
1262A LEU* 3.8 7.4 - - - +
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Residues in contact with ILE1259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1195A LEU* 4.3 15.5 - - + -
1197A TRP* 4.2 25.6 - - + -
1232A LEU* 4.6 13.0 - - + -
1236A LEU* 4.6 16.6 - - + +
1241A THR* 4.5 7.4 - - - +
1242A PRO* 3.3 42.8 - - + -
1246A LEU* 6.1 1.1 - - + -
1247A LEU* 4.7 2.9 - - + -
1250A ILE* 4.2 5.8 - - + -
1255A ALA 2.8 19.7 - - - +
1256A ARG* 3.5 6.1 - - - +
1258A TYR* 1.3 77.5 - - + +
1260A GLN* 1.3 58.8 - - + +
1261A SER 2.9 10.0 + - - -
1262A LEU* 3.5 16.6 + - - +
1291A LEU* 6.2 2.0 - - + -
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Residues in contact with GLN1260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1242A PRO* 6.1 0.7 - - - -
1247A LEU* 3.0 46.7 - - + +
1248A LYS* 5.2 2.4 - - - +
1256A ARG* 2.7 38.3 + - + +
1257A ASN* 2.9 10.1 + - - +
1259A ILE* 1.3 72.6 - - - +
1261A SER* 1.3 54.6 + - - +
1262A LEU 3.6 3.8 + - - +
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Residues in contact with SER1261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1257A ASN* 2.6 26.1 + - - -
1258A TYR* 2.7 19.1 + - - +
1260A GLN* 1.3 69.7 - - - +
1262A LEU* 1.3 77.1 + - - +
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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