Contacts of the strand formed by residues 278 - 283 (chain B) in PDB entry 6IEH
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 HIS 278 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B ASN* 3.2 51.4 + - - +
155B GLN* 5.2 1.3 - - - -
156B SER* 3.9 9.3 + - - +
247B ALA 3.2 7.2 + - - +
248B TRP* 3.2 36.0 - + + -
249B VAL 3.2 22.0 + - - -
275B ASP 5.2 0.2 - - - -
276B ASN 4.4 11.5 + - - -
277B VAL* 1.3 78.0 + - - +
279B TYR* 1.3 67.2 + - - +
302B GLN* 3.5 25.8 + - + -
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Residues in contact with TYR 279 (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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156B SER* 3.2 26.6 + - - +
157B VAL 3.3 7.7 + - - +
248B TRP* 3.9 2.9 - - - -
249B VAL* 3.5 18.2 - - + +
251B PHE* 4.2 11.4 - + + -
270B ILE* 5.1 3.4 - - + -
273B LEU* 3.5 35.1 - - + +
274B PRO 3.7 8.1 + - - -
277B VAL* 3.9 27.9 - - + +
278B HIS* 1.3 79.2 - - - +
280B VAL* 1.3 65.4 + - - +
281B PHE* 3.4 25.6 - + + -
296B ILE* 4.2 17.5 - - + -
300B HIS* 3.2 43.1 + + - -
302B GLN* 4.1 9.2 - - - -
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Residues in contact with VAL 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B VAL* 4.2 6.3 - - + -
157B VAL* 3.4 21.8 - - + +
159B VAL* 5.5 0.2 - - + -
170B CYS* 4.6 4.9 - - + +
171B ALA* 4.3 11.2 - - - +
174B ALA* 4.1 15.9 - - + -
248B TRP* 3.8 25.3 - - + -
249B VAL 3.3 4.5 + - - +
250B ILE* 3.5 22.9 - - + +
251B PHE 3.1 23.7 + - - -
279B TYR* 1.3 75.8 - - - +
281B PHE* 1.3 63.1 + - - +
282B LEU* 3.8 23.3 - - + -
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Residues in contact with PHE 281 (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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157B VAL 2.9 20.0 + - - -
158B LEU* 3.6 24.9 - - + -
159B VAL* 2.9 24.4 + - - +
251B PHE* 3.7 33.0 - + + -
254B ILE* 4.0 9.2 - - + -
270B ILE* 4.4 8.7 - - + -
279B TYR* 3.4 33.0 - + + -
280B VAL* 1.3 72.9 - - - +
282B LEU* 1.3 67.3 + - - +
292B PHE* 3.6 28.9 - + - -
296B ILE* 3.3 37.0 - - + -
304B CYS* 4.5 6.5 - - - -
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Residues in contact with LEU 282 (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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159B VAL* 3.9 16.4 - - + -
167B LYS* 3.3 44.4 - - + +
168B THR* 4.0 10.1 - - - +
170B CYS* 4.7 1.8 - - + -
171B ALA* 4.2 11.4 - - + -
187B PHE* 5.1 0.7 - - + -
250B ILE* 4.5 3.6 - - + -
251B PHE 2.9 12.5 + - - +
252B ASP* 2.8 31.4 - - + +
253B GLU* 3.1 4.7 + - - +
254B ILE* 2.8 26.2 + - - +
280B VAL* 3.8 21.5 - - + -
281B PHE* 1.3 81.5 - - - +
283B SER* 1.3 61.6 + - - +
1102B ATP 4.4 0.9 - - - +
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Residues in contact with SER 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B LEU* 4.0 9.9 - - - -
159B VAL 3.2 11.3 + - - +
160B SER* 4.5 0.2 - - - -
161B ALA 3.1 12.1 + - - -
167B LYS* 3.0 27.0 - - - +
253B GLU* 4.6 0.9 - - - +
254B ILE* 3.0 27.2 - - - +
255B HIS* 3.7 15.5 - - - +
282B LEU* 1.3 71.4 - - - +
284B ALA* 1.3 81.4 + - - +
286B ILE* 3.5 14.5 - - - +
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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