Contacts of the strand formed by residues 201 - 209 (chain A) in PDB entry 7ACN
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 LYS 201 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A ARG* 3.7 14.8 - - + +
58A GLY* 3.5 26.2 - - - +
200A PRO* 1.3 76.9 - - - +
202A VAL* 1.3 64.4 + - - +
203A ILE* 5.7 1.1 - - + -
235A GLY 2.9 17.0 + - - +
236A ALA* 3.2 10.9 - - + -
237A ILE 2.9 21.7 + - - -
308A ASP* 3.1 43.5 + - + +
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Residues in contact with VAL 202 (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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37A THR* 3.9 11.0 - - + +
39A SER* 3.6 26.0 - - - +
40A GLU* 4.5 4.5 - - + -
57A ARG* 4.0 26.5 - - - +
200A PRO* 4.3 5.8 - - + +
201A LYS* 1.3 79.1 - - - +
203A ILE* 1.3 64.2 + - - +
237A ILE* 3.4 11.0 - - + +
239A GLU* 3.8 13.0 - - + +
307A TYR* 3.5 31.0 - - + -
308A ASP* 2.8 38.1 + - - +
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Residues in contact with ILE 203 (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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201A LYS* 5.7 1.8 - - + -
202A VAL* 1.3 74.0 - - - +
204A GLY* 1.3 63.0 + - - +
205A VAL* 4.3 8.3 - - + -
228A LEU* 4.7 12.8 - - + -
232A GLY 4.0 19.5 - - - +
233A GLY* 4.3 7.0 - - - -
236A ALA* 3.9 24.0 - - + -
237A ILE 2.9 9.1 + - - +
238A VAL* 3.4 12.4 - - + +
239A GLU* 2.8 26.2 + - - +
307A TYR* 4.3 1.1 - - - -
308A ASP* 5.8 0.9 - - + -
309A GLN* 3.5 33.4 - - + +
311A ILE* 4.1 25.1 - - + -
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Residues in contact with GLY 204 (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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203A ILE* 1.3 74.1 - - - +
205A VAL* 1.3 62.4 + - - +
239A GLU 3.3 9.0 - - - -
241A HIS* 3.8 9.4 - - - -
307A TYR* 3.6 27.7 - - - +
309A GLN 2.9 10.1 + - - +
310A VAL* 3.2 6.0 - - - -
311A ILE 2.9 23.0 + - - +
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Residues in contact with VAL 205 (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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203A ILE* 4.3 8.1 - - + -
204A GLY* 1.3 77.8 - - - +
206A LYS* 1.3 61.7 + - - +
207A LEU* 3.7 13.5 + - + -
224A VAL* 4.5 19.3 - - + -
228A LEU* 5.6 0.2 - - + -
238A VAL* 3.7 25.1 - - + -
239A GLU 2.9 7.2 + - - +
240A TYR* 3.4 31.5 - - + +
241A HIS* 3.0 26.9 + - - +
311A ILE* 3.2 29.4 - - + +
313A ILE* 4.6 4.5 - - + -
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Residues in contact with LYS 206 (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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205A VAL* 1.3 70.6 - - - +
207A LEU* 1.3 65.0 + - - +
208A THR* 3.5 12.4 + - - +
241A HIS* 3.3 27.4 - - + +
242A GLY* 4.1 8.3 - - - -
243A PRO* 4.7 10.5 - - - -
310A VAL* 4.9 7.4 - - + -
311A ILE 2.8 13.6 + - - +
312A GLU* 2.7 43.4 + - + +
313A ILE 2.8 32.6 + - - +
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Residues in contact with LEU 207 (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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205A VAL* 4.0 22.7 - - + +
206A LYS* 1.3 72.0 - - - +
208A THR* 1.3 66.3 + - - +
220A VAL* 4.0 17.5 - - + -
240A TYR* 4.2 11.9 - - + -
241A HIS 2.9 12.9 + - - +
242A GLY* 3.4 13.5 - - - -
243A PRO 3.4 1.2 - - - -
244A GLY* 2.9 22.7 + - - -
245A VAL* 3.9 19.1 - - + +
248A ILE* 3.7 30.5 - - + -
270A PHE* 4.0 11.2 - - + -
313A ILE* 3.3 8.3 - - + -
315A LEU* 4.0 26.2 - - + -
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Residues in contact with THR 208 (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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206A LYS* 3.5 20.9 + - - -
207A LEU* 1.3 77.0 + - - +
209A GLY* 1.3 64.2 + - - +
243A PRO* 4.1 11.4 - - - +
244A GLY* 4.1 3.6 - - - +
312A GLU* 3.9 17.4 + - - +
313A ILE 2.8 7.4 + - - -
314A ASN* 3.4 29.8 - - + +
315A LEU* 2.8 30.0 + - - +
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Residues in contact with GLY 209 (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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208A THR* 1.3 78.8 - - - +
210A SER* 1.3 63.7 + - - -
243A PRO* 4.6 4.2 - - - +
244A GLY* 3.3 19.9 - - - +
247A SER* 4.4 0.5 - - - -
314A ASN* 3.7 5.6 - - - -
315A LEU* 4.0 0.2 - - - -
316A SER* 3.2 14.1 - - - -
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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