Contacts of the strand formed by residues 204 - 211 (chain A) in PDB entry 3ATI
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 204 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A ILE* 4.2 1.1 - - - -
122A SER* 3.5 23.8 + - - +
123A LEU 3.7 16.2 + - - +
124A PRO* 4.1 17.0 - - + -
125A THR* 4.9 16.9 - - - +
200A VAL* 3.2 6.8 - - - -
201A CYS 3.0 31.3 + - - +
202A SER* 3.7 13.5 - - - +
203A GLY* 1.3 86.2 - - - +
205A LEU* 1.3 60.6 + - - +
206A GLN* 3.2 14.9 + - - +
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Residues in contact with LEU 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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46A SER* 3.5 36.8 - - - +
48A ILE* 4.3 17.0 - - + -
54A VAL* 4.3 19.5 - - + -
121A ILE* 3.9 11.4 - - + +
122A SER 3.0 17.2 + - - +
123A LEU* 4.8 4.0 - - + -
124A PRO* 3.1 25.6 - - + +
198A PRO* 3.7 15.7 - - + -
199A VAL 3.8 4.7 - - - +
200A VAL* 4.1 6.3 - - + -
204A LYS* 1.3 69.6 - - - +
206A GLN* 1.3 57.5 + - - +
207A GLY 3.5 23.1 - - - +
208A ILE* 5.1 1.8 - - + -
227A VAL* 3.5 19.3 - - + +
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Residues in contact with GLN 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A PRO* 3.5 18.0 - - - +
126A SER* 2.9 27.0 + - - +
127A CYS* 3.8 4.0 - - - -
128A ALA* 3.3 39.5 + - + +
160A ILE* 5.1 0.2 - - + -
179A PHE* 3.3 17.7 - - + -
199A VAL 2.9 5.7 + - - -
201A CYS* 3.7 30.5 + - + +
204A LYS* 3.2 16.5 + - - +
205A LEU* 1.3 74.6 - - - +
207A GLY* 1.3 59.0 + - - +
226A LYS* 3.9 1.0 - - - +
227A VAL* 3.0 25.8 + - - -
228A CYS* 4.1 6.9 + - - +
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Residues in contact with GLY 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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179A PHE* 3.8 9.2 - - - -
198A PRO* 3.8 0.7 - - - +
199A VAL* 3.0 39.5 + - - +
205A LEU* 3.5 14.4 - - - +
206A GLN* 1.3 81.3 - - - +
208A ILE* 1.3 64.3 + - - +
224A TYR* 4.5 0.4 - - - -
225A THR 3.2 9.6 - - - -
227A VAL* 3.7 1.6 - - - -
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Residues in contact with ILE 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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46A SER* 6.0 0.9 - - - +
54A VAL* 3.4 32.5 - - + +
55A SER 3.7 3.1 - - - +
56A ALA* 3.7 15.7 - - + +
102A ASP 4.2 1.6 - - - +
103A ILE* 3.5 30.1 - - + -
196A GLY* 3.6 32.1 - - - +
197A GLY 3.3 4.3 - - - +
205A LEU* 5.1 3.1 - - + -
207A GLY* 1.3 79.6 - - - +
209A VAL* 1.3 70.6 + - - +
210A SER* 3.1 2.1 + - - -
224A TYR* 3.3 7.3 - - - +
225A THR* 3.0 37.8 + - - +
227A VAL* 3.8 13.5 - - + -
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Residues in contact with VAL 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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6A SZ4 3.7 27.1 - - + -
56A ALA* 3.9 0.9 - - - +
58A HIS* 3.9 3.1 + - - -
136A ILE* 4.2 17.3 - - + -
137A SER 4.9 1.8 - - - +
190A SER* 3.7 13.2 - - - +
194A ASP* 3.3 37.7 - - + +
195A SER* 3.7 4.2 - - - +
196A GLY* 2.9 25.8 + - - +
197A GLY* 2.9 25.9 + - - +
198A PRO 4.5 1.6 - - - +
208A ILE* 1.3 71.6 - - - +
210A SER* 1.3 60.8 + - - +
224A TYR* 3.6 20.2 - - + -
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Residues in contact with SER 210 (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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6A SZ4 4.5 7.8 - - - -
56A ALA* 5.6 0.2 - - - -
58A HIS* 3.2 22.7 + - - -
99A LEU* 4.2 3.1 + - - +
102A ASP* 2.6 32.7 + - - +
178A MET* 6.0 1.4 - - - +
208A ILE 3.1 3.9 + - - -
209A VAL* 1.3 76.1 - - - +
211A TRP* 1.3 81.6 + - - +
223A VAL 3.2 13.7 + - - -
224A TYR* 4.1 0.9 - - - -
225A THR* 3.7 21.5 + - - -
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Residues in contact with TRP 211 (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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6A SZ4 3.6 22.2 - - - -
98A THR 5.1 3.6 - - - -
99A LEU* 3.4 30.0 - - + +
170A TYR* 3.6 40.6 - + - -
173A GLN* 3.8 39.0 - - + -
174A ILE* 3.8 19.7 - - + -
178A MET* 3.6 17.9 - - + +
210A SER* 1.3 102.1 - - - +
212A GLY* 1.3 80.3 + - - +
213A SER* 5.9 0.2 - - - -
223A VAL* 2.7 56.8 + - + +
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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