Contacts of the strand formed by residues 246 - 250 (chain C) in PDB entry 4DEP
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 CYS 246 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226C HIS 4.6 1.6 - - - -
244C ILE 3.5 1.6 + - - -
245C PRO* 1.3 70.7 - - - +
247C THR* 1.3 58.5 + - - +
248C VAL* 4.1 4.8 - - - +
260C VAL* 3.9 23.1 - - + +
262C TRP* 3.3 23.1 - - + +
292C ARG 3.8 2.3 - - - +
293C THR* 3.6 1.4 - - - -
294C GLN* 2.9 42.2 + - - +
312C CYS* 2.0 50.9 - - - -
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Residues in contact with THR 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ARG* 5.4 5.6 - - - +
402B NAG 4.3 8.1 + - - +
225C ILE* 3.5 1.0 - - - +
226C HIS* 2.7 62.7 + - + +
245C PRO* 4.2 9.5 - - - +
246C CYS* 1.3 71.7 - - - +
248C VAL* 1.3 68.2 + - - +
291C THR* 4.2 17.3 - - + -
292C ARG 3.8 1.8 - - - -
293C THR* 3.2 33.9 - - + +
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Residues in contact with VAL 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C PRO* 3.9 14.6 - - + -
224C VAL 3.3 12.8 - - - +
225C ILE* 4.4 11.4 - - + +
246C CYS* 4.1 18.4 - - - -
247C THR* 1.3 84.5 - - - +
249C TYR* 1.3 65.2 + - - +
250C PHE* 3.9 21.3 + - + -
260C VAL* 3.9 19.3 - - + -
291C THR* 3.5 6.0 - - - +
292C ARG 3.0 31.7 + - - +
312C CYS* 4.4 0.7 - - - -
314C ALA* 3.7 26.5 - - + -
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Residues in contact with TYR 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ARG* 4.8 25.8 - - - +
222C PRO 4.8 0.3 - - - +
223C PRO* 4.0 3.3 - - - +
224C VAL* 2.7 49.5 + - + +
226C HIS* 6.5 0.7 - - + -
248C VAL* 1.3 73.6 - - - +
250C PHE* 1.3 62.7 + - - +
251C SER 3.9 2.6 + - - -
290C GLU 3.6 5.8 - - - +
291C THR* 4.7 4.9 - - + +
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Residues in contact with PHE 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C VAL 5.8 0.4 - - - -
223C PRO* 4.0 23.3 - - + -
248C VAL* 3.9 20.4 - - + -
249C TYR* 1.3 71.9 - - - +
251C SER* 1.3 68.0 + - - +
252C PHE* 3.5 1.4 + - - -
258C ASN* 3.4 46.3 + - + +
259C GLU 3.3 22.2 - - - -
260C VAL* 3.7 20.2 - - + -
289C ASP* 3.6 1.9 - - - -
290C GLU* 2.8 40.1 + - + +
292C ARG* 3.9 21.5 - - + -
314C ALA* 4.0 0.7 - - + -
315C ARG 3.6 20.6 - - - -
316C SER* 3.9 12.1 - - - -
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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