Contacts of the strand formed by residues 1228 - 1232 (chain A) in PDB entry 1Y8Z
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 SER1228 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1197A ASN* 2.9 19.3 + - - +
1198A ILE* 4.6 10.3 - - - -
1199A ASN* 2.8 30.4 + - - +
1218A HIS* 4.7 0.9 - - - -
1226A GLY 4.9 0.7 + - - -
1227A LYS* 1.3 74.4 - - - +
1229A THR* 1.3 63.0 + - - +
1230A VAL* 5.4 1.3 - - - -
1262A ASN 5.6 0.4 - - - -
1263A LEU* 3.1 37.0 + - - -
1264A ALA 3.4 17.0 + - - -
1265A PRO* 4.1 1.2 - - - +
1267A GLN* 6.0 0.4 - - - -
1270A GLN* 6.4 1.1 - - - -
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Residues in contact with THR1229 (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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1199A ASN* 3.3 2.8 - - - +
1214A MET* 3.7 26.5 - - + +
1218A HIS* 2.8 43.2 + - + -
1222A LEU* 3.0 22.7 - - - +
1228A SER* 1.3 72.8 - - - +
1230A VAL* 1.3 70.9 + - - +
1231A MET* 4.1 14.4 - - + -
1268A PRO 4.3 1.9 + - - +
1269A ALA* 3.5 10.6 - - + -
1270A GLN* 2.9 28.1 + - - +
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Residues in contact with VAL1230 (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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1198A ILE* 4.6 8.5 - - + -
1199A ASN 2.8 9.1 + - - +
1200A ARG* 3.3 39.6 - - + +
1201A TRP* 2.7 31.5 + - - +
1228A SER* 5.4 1.8 - - - -
1229A THR* 1.3 80.9 - - - +
1231A MET* 1.3 62.5 + - - +
1232A GLU* 4.1 14.4 - - + -
1261A MET* 3.8 19.5 - - + -
1263A LEU* 3.8 29.4 - - + -
1270A GLN* 3.3 11.7 - - + +
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Residues in contact with MET1231 (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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1201A TRP* 3.4 35.9 - - + -
1211A PHE* 3.6 42.6 - - + +
1214A MET* 3.8 16.8 - - + -
1215A PHE* 3.6 36.6 - - + -
1229A THR* 4.1 6.3 - - + -
1230A VAL* 1.3 78.1 - - - +
1232A GLU* 1.3 62.7 + - - +
1234A LEU* 4.2 4.0 - - + -
1269A ALA* 4.2 4.7 - - + -
1270A GLN 2.8 8.5 + - - -
1271A ILE* 3.4 22.3 - - + +
1272A LEU 2.8 24.3 + - - -
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Residues in contact with GLU1232 (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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1200A ARG* 3.0 27.9 + - + +
1201A TRP* 2.7 17.3 + - - +
1202A ILE* 3.4 5.9 - - + -
1203A GLY 3.1 25.3 + - - +
1230A VAL* 4.1 11.7 - - + -
1231A MET* 1.3 75.5 - - - +
1233A GLY* 1.3 61.5 + - - +
1234A LEU 3.5 0.4 - - - -
1272A LEU* 3.3 22.5 - - + +
1275A TYR* 3.4 23.7 - - + +
1280A MET* 3.5 11.7 - - - +
1283A ARG* 2.7 46.4 + - - +
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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