Contacts of the strand formed by residues 1245 - 1249 (chain B) in PDB entry 4DDI
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 ASN1245 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1071B LYS* 5.8 0.2 - - - -
1233B VAL 3.4 2.3 - - - +
1234B GLU* 4.0 0.4 - - - -
1235B TYR* 2.9 46.9 + - + +
1237B ASP* 5.3 2.3 - - - +
1239B GLY* 6.2 0.2 - - - -
1243B THR* 3.8 21.2 + - - +
1244B THR* 1.3 70.2 - - - +
1246B PRO* 1.3 69.9 - - + +
1247B HIS* 3.5 21.5 + - + +
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Residues in contact with PRO1246 (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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1078B LYS* 5.1 6.5 - - - +
1232B GLN* 3.9 18.8 - - + +
1233B VAL 3.7 3.8 - - - +
1234B GLU* 3.2 24.2 - - - +
1244B THR 3.2 8.5 - - - +
1245B ASN* 1.3 88.0 - - + +
1247B HIS* 1.3 68.2 + - - +
1248B ILE* 4.2 2.7 - - + -
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Residues in contact with HIS1247 (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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1231B ILE 3.3 2.6 - - - +
1232B GLN* 3.2 4.9 - - - +
1233B VAL* 2.9 50.3 + - + +
1235B TYR* 4.2 17.9 - + + +
1245B ASN* 3.5 33.0 + - + +
1246B PRO* 1.3 74.9 + - - +
1248B ILE* 1.3 64.0 + - - +
1249B PHE* 3.7 32.7 + + + -
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Residues in contact with ILE1248 (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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1231B ILE 3.4 4.0 - - - +
1232B GLN* 3.3 28.5 - - - +
1246B PRO* 4.2 2.4 - - + -
1247B HIS* 1.3 71.8 - - - +
1249B PHE* 1.3 73.1 + - - +
1250B PRO 3.7 11.4 - - - +
1251B GLU* 3.4 15.8 + - - +
1252B GLY* 3.8 17.0 - - - +
1253B SER* 3.0 30.5 - - - +
1254B GLU* 5.1 1.3 - - + -
1255B PRO* 3.6 21.3 - - + -
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Residues in contact with PHE1249 (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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1217B HIS* 3.4 39.0 - + - -
1220B ILE* 4.9 8.5 - - + -
1221B ILE* 3.9 24.0 - - + -
1224B ALA* 4.6 2.4 - - + +
1229B VAL 3.7 1.4 - - - +
1230B SER* 3.2 6.8 - - - -
1231B ILE* 2.9 58.7 + - + +
1233B VAL* 4.4 9.2 - - + -
1247B HIS* 3.8 35.2 - + + -
1248B ILE* 1.3 85.7 - - - +
1250B PRO* 1.3 68.4 - - + +
1251B GLU* 4.9 5.2 - - + -
1253B SER* 4.0 0.9 - - - -
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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