Contacts of the strand formed by residues 229 - 234 (chain A) in PDB entry 4GGA
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 ILE 229 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A ARG* 5.1 2.1 - - - +
187A LEU* 4.1 1.7 - - - +
189A LEU* 3.5 14.4 - - - +
201A ALA* 3.4 24.4 - - + +
203A ASP 3.0 12.9 + - - +
204A ASN 3.2 11.7 - - - +
205A SER* 3.2 49.4 - - - +
206A VAL* 3.6 12.6 - - + +
220A LEU* 3.8 6.3 - - + -
222A MET* 4.1 11.4 - - + -
228A TYR* 1.3 85.0 - - - +
230A SER* 1.3 62.1 + - - +
231A SER 3.9 14.6 - - - +
232A VAL* 4.4 0.7 - - + -
243A VAL* 4.0 15.3 - - + -
244A GLY 3.7 11.2 - - - +
245A THR* 4.5 1.8 - - + +
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Residues in contact with SER 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A LEU* 3.5 26.7 - - - +
188A ASN 3.4 17.7 + - - -
189A LEU* 4.1 4.7 - - - -
228A TYR* 3.7 7.8 + - - -
229A ILE* 1.3 74.2 - - - +
231A SER* 1.3 64.2 + - - +
244A GLY 2.9 6.5 + - - -
245A THR 3.0 28.0 + - - -
246A SER 4.2 2.2 - - - -
270A ARG* 4.6 4.9 - - - -
271A VAL 2.5 25.8 + - - -
272A GLY* 3.5 4.9 - - - +
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Residues in contact with SER 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ASN* 3.2 13.9 - - - -
189A LEU* 4.5 0.6 - - - +
229A ILE* 3.8 3.6 - - - +
230A SER* 1.3 79.9 - - - +
232A VAL* 1.3 67.0 + - - +
243A VAL* 3.3 5.7 - - - +
244A GLY* 2.8 30.2 + - - +
271A VAL 2.9 16.0 + - - -
272A GLY 3.5 18.8 - - - -
273A SER* 3.9 1.8 - - - -
274A LEU* 3.3 27.2 - - - +
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Residues in contact with VAL 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ASN* 3.1 10.0 + - - +
189A LEU 3.7 25.8 - - - +
190A VAL* 3.8 5.3 - - - +
191A ASP* 3.9 23.2 - - + +
199A ALA* 4.0 8.1 - - + +
201A ALA* 4.3 14.1 - - + +
206A VAL* 4.3 31.0 - - + -
229A ILE* 4.4 1.1 - - + -
231A SER* 1.3 81.9 - - - +
233A ALA* 1.3 64.9 + - - +
241A LEU* 4.2 8.3 - - + -
242A ALA 3.3 9.6 - - - +
243A VAL* 4.5 5.2 - - + -
274A LEU* 3.8 4.4 - - - +
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Residues in contact with ALA 233 (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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191A ASP* 3.4 10.3 - - - +
232A VAL* 1.3 77.7 - - - +
234A TRP* 1.3 60.6 + - - +
241A LEU* 3.6 4.7 - - - +
242A ALA* 2.8 35.2 + - + -
274A LEU* 3.7 34.3 - - + +
275A SER* 5.1 1.6 - - - -
276A TRP* 3.0 24.7 + - + +
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Residues in contact with TRP 234 (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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191A ASP* 2.8 51.4 + - + +
193A SER* 3.4 32.3 - - - -
197A VAL* 3.3 37.8 + - + -
199A ALA* 3.6 17.2 - - + +
208A LEU* 3.9 12.3 - - + -
233A ALA* 1.3 72.8 - - - +
235A ILE* 1.3 69.8 + - - +
236A LYS 3.8 0.2 + - - -
238A GLY* 3.4 27.1 - - - -
240A TYR 3.4 22.4 - - - -
241A LEU* 3.7 12.3 - - + -
255A VAL* 3.8 34.1 - - + -
276A TRP* 3.2 13.1 - - - +
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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