Contacts of the strand formed by residues 272 - 276 (chain B) in PDB entry 1I43
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 GLY 272 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B LEU 4.5 0.2 - - - -
134B LEU* 3.3 24.1 - - - +
135B MET 3.0 27.9 + - - -
137B SER 3.3 22.9 - - - -
138B GLY* 3.6 4.7 - - - -
141B ALA* 4.2 4.9 - - - -
257B HIS 4.3 0.2 - - - -
259B ALA* 5.1 1.1 - - - +
271B ALA* 1.3 74.5 - - - +
273B CYS* 1.3 61.6 + - - +
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Residues in contact with CYS 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ILE* 3.5 46.2 - - - -
132B THR* 4.4 5.2 - - - -
133B LEU 3.7 2.7 - - - -
134B LEU* 4.9 2.7 - - - -
141B ALA* 3.9 4.3 - - - +
256B LEU* 2.9 26.2 - - - +
257B HIS* 3.1 35.6 + - + +
259B ALA* 4.8 2.7 - - + +
263B LEU* 4.0 13.9 - - + -
272B GLY* 1.3 78.1 - - - +
274B ILE* 1.3 67.3 + - - +
275B SER* 4.4 2.7 - - - -
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Residues in contact with ILE 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B THR* 3.2 3.1 - - - +
133B LEU* 2.7 44.5 + - + +
135B MET* 3.9 17.3 - - + -
141B ALA* 3.3 42.8 - - + +
145B MET* 3.9 15.0 - - + -
254B LEU* 4.5 15.7 - - + -
255B VAL 3.7 4.9 - - - +
256B LEU* 4.1 9.0 - - + +
273B CYS* 1.3 82.0 - - - +
275B SER* 1.3 64.0 + - - +
281B VAL* 3.9 10.5 - - + +
284B ILE* 4.0 25.8 - - + -
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Residues in contact with SER 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ILE* 3.7 14.4 - - - +
127B GLU* 4.1 8.8 + - - +
129B ALA* 3.8 14.1 - - - -
131B SER 3.5 4.7 - - - -
132B THR* 3.1 21.5 + - - +
248B LEU* 4.2 0.3 - - - +
254B LEU* 3.5 6.8 - - - +
255B VAL* 2.9 52.0 + - - +
257B HIS* 5.2 1.9 - - - -
273B CYS* 4.7 2.1 - - - -
274B ILE* 1.3 78.5 + - - +
276B GLY* 1.3 58.7 + - - +
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Residues in contact with GLY 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ALA* 3.8 2.0 - - - +
130B GLU 3.4 6.7 + - - -
131B SER 3.0 30.2 + - - +
248B LEU* 4.2 11.2 - - - -
253B ASP 3.7 6.3 - - - -
254B LEU* 4.3 4.9 - - - -
275B SER* 1.3 75.3 - - - +
277B PRO* 1.3 78.3 - - - +
281B VAL* 4.7 3.0 - - - +
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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