Contacts of the strand formed by residues 197 - 203 (chain A) in PDB entry 1XGS
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 VAL 197 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A ALA* 3.5 31.4 - - + -
147A ILE* 4.0 13.0 - - + -
149A ASN* 2.9 45.7 + - - +
150A LEU* 3.7 28.3 - - + -
196A GLN* 1.3 80.4 + - - +
198A ILE* 1.3 65.8 - - - +
268A LEU* 4.2 20.5 - - + +
269A LYS 3.2 13.5 - - - +
270A GLU* 4.2 3.6 - - - -
170B TYR* 5.7 1.9 - - - -
172B PRO* 4.9 1.9 - - + +
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Residues in contact with ILE 198 (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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196A GLN* 5.4 3.1 - - + +
197A VAL* 1.3 78.1 - - - +
199A GLU* 1.3 66.5 + - - +
200A VAL* 3.8 10.7 + - + -
268A LEU* 3.4 5.6 - - - -
269A LYS* 2.9 63.8 + - - +
271A ILE* 4.0 37.7 - - + +
170B TYR* 6.4 1.1 - - - -
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Residues in contact with GLU 199 (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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198A ILE* 1.3 77.5 - - - +
200A VAL* 1.3 65.7 + - - +
201A PRO* 4.9 0.2 - - - +
263A TYR* 6.0 1.2 - - - -
265A TYR* 5.6 2.8 - - - -
266A PRO* 4.0 34.1 - - + +
267A VAL 3.4 4.3 - - - -
268A LEU* 3.7 17.2 - - + +
129B LYS* 5.3 0.7 + - - -
170B TYR* 2.5 45.2 + - + -
172B PRO* 4.0 10.0 - - - +
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Residues in contact with VAL 200 (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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59A ILE* 5.1 2.2 - - + -
198A ILE* 4.1 15.0 - - + +
199A GLU* 1.3 80.1 - - - +
201A PRO* 1.3 77.7 - - + +
266A PRO* 3.3 6.7 - - - +
267A VAL* 2.9 58.2 + - + +
269A LYS* 3.8 38.4 - - + -
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Residues in contact with PRO 201 (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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199A GLU 4.9 0.4 - - - +
200A VAL* 1.3 98.3 - - + +
202A PRO* 1.3 69.3 - - + +
203A THR* 5.6 0.7 - - - +
266A PRO* 5.1 1.6 - - + -
267A VAL* 4.7 1.0 - - - +
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Residues in contact with PRO 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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63A TYR* 5.2 6.5 - - + -
66A TYR* 5.5 4.5 - - + -
200A VAL 4.2 0.2 - - - -
201A PRO* 1.3 87.8 - - + +
203A THR* 1.3 62.1 + - - +
204A LEU* 3.7 34.5 + - + -
267A VAL* 3.2 37.3 + - + +
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Residues in contact with THR 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 PRO* 5.6 0.7 - - - +
202A PRO* 1.3 73.6 - - - +
204A LEU* 1.3 63.6 + - - +
205A ILE 3.5 9.6 - - - +
206A TYR* 3.6 35.2 + - + -
237A TYR* 4.7 4.2 - - - +
257A GLU* 5.6 0.9 - - - +
264A GLY* 3.6 7.8 - - - -
265A TYR 3.5 28.7 - - - +
266A PRO* 3.8 22.9 - - - +
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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