Contacts of the strand formed by residues 218 - 222 (chain A) in PDB entry 4IYM
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 ALA 218 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A VAL* 4.3 8.1 - - + -
140A ILE 3.8 1.6 + - - -
141A GLY* 3.4 1.8 - - - -
142A ALA 2.9 26.7 + - - +
216A ILE* 3.6 2.8 - - - +
217A ALA* 1.3 80.5 - - - +
219A VAL* 1.3 66.7 + - - +
240A LYS* 4.7 0.4 - - - +
241A ARG* 3.3 28.9 - - + -
469A PHE* 3.8 8.7 - - + -
470A TRP* 3.8 25.4 - - + -
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Residues in contact with VAL 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A ALA 3.2 8.3 - - - +
144A ILE* 3.8 28.9 - - + -
210A ILE* 4.3 15.0 - - + -
211A LEU* 4.2 14.6 - - + -
216A ILE* 4.4 2.9 - - + -
218A ALA* 1.3 80.2 - - - +
220A SER* 1.3 66.3 + - - +
231A VAL* 4.1 15.9 - - + -
235A ALA* 4.6 7.9 - - + -
240A LYS* 3.8 26.7 - - + -
241A ARG 2.9 8.9 + - - +
242A ALA* 3.4 5.7 - - + +
243A GLN 3.2 23.4 + - - +
244A CYS* 5.3 0.6 - - - -
469A PHE* 3.4 5.8 - - - -
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Residues in contact with SER 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A ALA 2.9 8.3 + - - -
143A GLY* 3.2 1.9 - - - -
144A ILE* 2.9 26.5 + - - +
157A MSE 3.4 21.9 - - - +
219A VAL* 1.3 75.1 - - - +
221A PHE* 1.3 58.8 + - - +
243A GLN* 2.8 32.7 + - - -
461A GLN* 3.0 18.2 + - - -
469A PHE* 4.8 0.2 - - - -
470A TRP* 4.1 16.6 - - - -
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Residues in contact with PHE 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A ILE* 3.5 34.3 - - + -
157A MSE 3.8 0.2 - - - -
220A SER* 1.3 75.1 + - - +
222A VAL* 1.3 71.6 + - - +
223A GLY* 3.3 30.5 - - - -
224A SER 3.9 1.1 - - - -
227A ILE* 3.4 37.5 - - + -
228A ALA* 3.5 33.2 - - + -
231A VAL* 3.7 22.2 - - + -
243A GLN 2.9 9.1 + - - -
244A CYS* 3.4 19.7 - - + -
245A PHE* 2.9 28.7 + - - -
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Residues in contact with VAL 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A ILE 3.1 11.7 + - - +
145A THR 3.8 1.4 - - - -
146A PRO* 3.3 26.4 - - + +
153A ILE* 3.6 42.4 - - + -
156A TRP* 4.2 12.3 - - + -
157A MSE 3.7 6.1 - - + -
221A PHE* 1.3 88.4 - - - +
223A GLY* 1.3 60.3 + - - +
245A PHE* 3.5 19.1 - - + +
246A GLY 6.0 0.7 - - - +
279A CYS* 5.9 7.4 - - - -
448A PHE* 6.1 1.6 - - + -
461A GLN* 3.5 22.7 - - - +
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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