Contacts of the strand formed by residues 220 - 225 (chain A) in PDB entry 3CQ6
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 LEU 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187A ILE* 4.0 20.4 - - + -
194A VAL* 3.6 12.8 - - + +
196A VAL* 3.4 33.4 - - + -
209A ALA* 3.4 27.8 - - + +
212A LEU* 3.7 24.0 - - + +
213A LEU* 3.3 30.1 - - + +
216A TYR* 3.1 21.0 + - + +
217A PRO 4.8 1.0 - - - +
219A LYS* 1.3 77.1 - - - +
221A VAL* 1.3 70.1 + - - +
222A VAL* 4.2 4.9 - - + -
242A ALA* 3.8 6.4 - - - +
243A ASN 4.8 0.5 + - - -
246A PHE* 3.9 6.3 - - - -
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Residues in contact with VAL 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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105A LEU* 3.9 24.2 - - + -
193A ILE* 4.9 7.0 - - + -
194A VAL 3.1 9.4 + - - +
195A ILE* 3.5 8.9 - - + +
196A VAL 2.9 25.6 + - - +
219A LYS 5.0 0.4 - - - +
220A LEU* 1.3 79.5 - - - +
222A VAL* 1.3 66.6 + - - +
223A SER* 3.8 1.0 + - - +
240A PHE* 3.5 38.8 - - + -
241A VAL 3.8 3.4 - - - -
242A ALA* 4.1 1.1 - - + -
246A PHE* 3.5 39.3 - - + -
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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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196A VAL* 3.6 3.4 - - + +
198A GLU* 3.5 37.2 - - + +
209A ALA* 3.8 35.9 - - + +
210A THR* 3.8 18.8 - - + +
213A LEU* 4.4 3.4 - - + -
220A LEU* 4.2 11.7 - - + -
221A VAL* 1.3 74.8 - - - +
223A SER* 1.3 60.2 + - - +
224A ARG* 3.9 13.8 + - + +
240A PHE* 3.1 5.4 - - - -
241A VAL* 2.8 44.0 + - + +
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Residues in contact with SER 223 (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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98A SER* 4.0 14.4 + - - -
101A ILE* 4.2 8.8 - - - +
102A LEU* 4.1 14.8 - - - +
195A ILE* 4.2 16.4 - - - -
196A VAL 2.8 15.5 + - - -
197A ASP* 4.2 14.9 + - - -
198A GLU* 2.7 35.3 + - - +
221A VAL* 3.8 1.9 + - - -
222A VAL* 1.3 72.3 - - - +
224A ARG* 1.3 61.9 + - - +
239A TYR 3.7 6.6 + - - -
240A PHE* 4.1 6.5 - - - -
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Residues in contact with ARG 224 (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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78A TYR* 4.1 0.8 + - - -
79A ILE* 4.0 13.3 - - - +
82A GLN* 4.0 18.0 - - - +
83A THR* 3.9 10.7 - - - +
98A SER* 2.9 15.6 + - - -
198A GLU* 2.9 41.0 + - - -
199A ALA* 4.8 1.1 - - - +
201A ALA* 3.6 16.3 - - - +
202A GLU* 2.8 35.4 + - - +
208A SER* 3.4 12.9 + - - -
210A THR* 4.7 0.4 - - - +
222A VAL* 4.0 16.2 - - + +
223A SER* 1.3 81.6 + - - +
225A THR* 1.3 62.2 + - - +
239A TYR* 2.8 64.5 + - + +
241A VAL* 4.4 5.2 - - + -
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Residues in contact with THR 225 (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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98A SER* 3.5 3.8 - - - -
198A GLU 5.1 0.4 + - - -
199A ALA* 3.6 38.3 + - + +
202A GLU* 4.7 11.3 + - - +
224A ARG* 1.3 77.9 - - - +
226A MET* 1.3 70.1 + - - +
227A SER* 2.8 18.9 + - - +
228A LLP 2.7 46.2 + - + +
229A ALA 5.7 0.7 + - - -
230A PHE* 4.4 9.0 + - - +
237A LEU 3.6 7.4 + - - -
238A GLY* 4.1 0.7 - - - -
239A TYR* 4.2 8.4 + - - -
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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