Contacts of the strand formed by residues 238 - 244 (chain A) in PDB entry 5IWM
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 ARG 238 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A ARG* 3.2 18.0 + - - +
233A ALA* 3.6 4.6 + - - -
236A THR* 3.1 21.4 + - - +
237A GLY* 1.3 86.7 - - - +
239A GLY* 1.3 59.2 + - - +
332A GLY 5.7 0.4 + - - -
333A VAL 3.2 9.5 + - - +
334A ASN* 3.5 39.4 + - - +
345A LEU* 4.2 18.4 - - + -
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Residues in contact with GLY 239 (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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229A GLY 4.0 8.3 - - - -
232A ARG* 4.6 9.2 - - - -
233A ALA* 4.0 12.3 - - - +
238A ARG* 1.3 75.7 - - - +
240A SER* 1.3 59.6 + - - -
241A ILE* 4.0 0.4 - - - -
331A PHE 3.6 1.2 - - - +
332A GLY* 3.7 1.7 - - - -
333A VAL* 2.8 38.4 + - - +
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Residues in contact with SER 240 (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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229A GLY* 3.5 18.9 + - - -
232A ARG* 5.7 1.4 - - - +
239A GLY* 1.3 71.6 - - - -
241A ILE* 1.3 61.9 + - - +
242A GLN* 4.0 12.7 + - - +
330A SER* 3.9 20.4 + - - -
331A PHE 3.8 4.2 + - - -
332A GLY* 4.7 4.5 - - - -
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Residues in contact with ILE 241 (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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184A PRO* 5.2 0.7 - - + -
216A PRO* 3.8 20.2 - - + -
218A PHE* 5.3 2.2 - - + -
224A ILE* 3.6 39.0 - - + -
229A GLY* 3.9 19.5 - - - +
230A ILE* 3.7 25.1 - - + +
233A ALA* 4.7 2.9 - - + -
234A TYR* 6.2 1.3 - - + -
239A GLY 4.9 0.2 - - - +
240A SER* 1.3 76.6 + - - +
242A GLN* 1.3 65.4 + - - +
243A MET* 3.6 6.1 + - + +
330A SER* 3.2 4.7 - - - -
331A PHE* 2.8 46.1 + - + +
333A VAL* 3.8 25.8 - - + -
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Residues in contact with GLN 242 (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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224A ILE* 3.3 6.1 - - - +
225A LEU* 3.1 58.2 + - + +
240A SER* 4.0 15.7 + - - +
241A ILE* 1.3 72.0 - - - +
243A MET* 1.3 63.4 + - - +
328A GLN* 3.6 23.6 + - - +
329A THR* 4.3 0.4 - - - -
330A SER* 3.6 28.6 + - - -
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Residues in contact with MET 243 (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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218A PHE* 3.6 40.8 - - + -
223A LEU 3.3 6.5 - - - +
224A ILE* 4.7 0.4 - - + +
241A ILE* 3.6 4.9 + - + +
242A GLN* 1.3 73.7 - - - +
244A ARG* 1.3 61.1 + - - +
265A PRO* 4.0 19.0 - - + +
266A PHE* 3.8 37.0 - - - +
328A GLN* 3.3 8.5 - - - +
329A THR* 3.0 50.1 + - + +
330A SER 4.1 2.9 - - - +
331A PHE* 4.0 30.1 - - + +
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Residues in contact with ARG 244 (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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222A GLY* 3.6 2.4 - - - -
223A LEU* 2.6 58.5 + - + +
225A LEU* 3.4 45.0 - - + +
243A MET* 1.3 76.9 - - - +
245A SER* 1.3 71.3 + - - +
265A PRO* 4.6 5.6 - - - +
319A ASN* 5.2 5.3 + - - -
322A TYR* 3.4 46.0 - - + +
327A LEU 4.0 3.4 - - - -
328A GLN* 2.7 31.2 + - + +
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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