Contacts of the strand formed by residues 204 - 208 (chain C) in PDB entry 5I4A
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 TYR 204 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156C PRO* 3.4 8.5 - - - +
157C ALA* 2.9 27.4 + - + -
167C LEU* 4.2 24.9 - - + -
168C TYR 3.6 2.0 - - - -
169C ASN* 3.3 33.3 + - + -
176C PHE* 4.0 17.4 - + - -
186C LEU* 3.7 17.9 - - + -
188C ILE* 3.7 28.8 - - + +
198C VAL* 3.9 21.8 - - + +
200C TYR* 3.3 26.0 - - + -
201C PRO* 3.2 14.3 + - + +
202C GLU 3.2 1.6 - - - +
203C ASN* 1.3 78.5 - - + +
205C LEU* 1.3 61.3 + - - +
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Residues in contact with LEU 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C TYR* 4.5 8.1 - - + +
127C HIS* 5.7 3.1 - - + +
152C LEU* 4.2 26.0 - - + -
153C SER* 3.5 19.7 - - - +
154C LYS 4.8 2.0 - - - +
155C GLU* 3.3 31.0 - - - +
156C PRO* 3.7 11.0 - - + -
157C ALA 4.5 0.7 - - - +
167C LEU* 3.3 9.6 - - - -
168C TYR* 2.7 37.4 + - + +
170C ILE* 3.8 26.0 - - + -
202C GLU 5.4 2.2 - - - +
204C TYR* 1.3 74.8 - - - +
206C PHE* 1.3 64.5 + - - +
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Residues in contact with PHE 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C LEU* 3.1 7.3 - - - -
153C SER* 2.7 48.4 + - - -
157C ALA* 3.4 38.8 - - + -
160C SER* 4.3 1.6 - - - -
162C ILE 3.8 11.9 - - - -
163C LYS* 3.5 25.4 - - + -
164C SER* 3.1 41.3 - - - -
166C TYR 3.7 9.2 - - - -
167C LEU* 3.5 19.5 - - + -
178C TYR* 3.6 24.9 - + + -
205C LEU* 1.3 72.2 - - - +
207C ASN* 1.3 59.5 + - - +
208C PHE* 3.7 14.8 - - + -
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Residues in contact with ASN 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C LYS* 3.7 27.9 - - - +
150C THR* 3.6 12.2 - - - +
151C PHE 3.0 16.7 + - - +
152C LEU* 3.5 17.4 - - + +
164C SER* 3.3 17.8 + - - -
166C TYR* 3.3 25.4 + - + +
167C LEU 5.1 0.2 - - - -
168C TYR* 4.3 12.1 - - + +
175C SER* 5.0 4.1 + - - +
205C LEU 3.7 1.0 + - - -
206C PHE* 1.3 72.6 - - - +
208C PHE* 1.3 66.8 + - - +
209C THR* 4.1 11.8 + - - +
212C ASP* 3.9 2.9 - - - +
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Residues in contact with PHE 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C VAL* 3.8 21.1 - - + -
151C PHE* 2.7 49.3 + - + +
152C LEU 3.9 2.0 - - - -
153C SER* 3.5 26.2 - - - -
162C ILE* 3.6 34.8 - - + -
163C LYS 3.5 23.6 - - - -
164C SER* 3.7 14.1 - - - -
206C PHE* 3.7 18.6 - - + -
207C ASN* 1.3 75.8 + - - +
209C THR* 1.3 65.2 + - - +
212C ASP* 3.8 10.3 - - + -
216C TYR* 4.6 2.2 - + - -
218C PHE* 4.1 24.7 - + + -
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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