Contacts of the strand formed by residues 210 - 215 (chain A) in PDB entry 3SDI
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 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A THR 3.7 4.7 - - - +
51A GLU* 3.8 12.8 - - + -
52A LYS* 4.1 9.0 - - - -
194A LEU* 4.3 9.9 - - + -
197A LEU* 3.7 23.6 - - + -
202A VAL* 4.2 4.3 - - + -
206A PHE* 3.4 41.1 - - + -
207A ASN 3.2 16.1 + - - +
208A GLY 3.9 7.4 - - - +
209A THR* 1.3 92.1 - - + +
211A GLU* 1.3 63.1 + - - +
212A LEU* 3.6 28.5 - - + -
229A ILE* 3.7 22.7 - - + +
233A LEU* 6.1 0.4 - - + -
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Residues in contact with GLU 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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48A ILE 4.1 0.5 - - - +
49A ALA* 3.2 5.0 - - - +
50A THR* 2.8 49.0 + - + +
52A LYS* 3.5 29.2 + - + +
62A GLU* 6.2 0.2 - - - -
64A LEU 3.9 3.3 - - - +
65A SER* 3.3 28.2 + - - -
66A LYS* 2.9 35.4 + - - +
67A VAL* 3.8 18.8 - - + +
210A ILE* 1.3 74.7 - - - +
212A LEU* 1.3 62.2 + - - +
223A LYS* 3.8 14.0 - - + -
229A ILE* 4.9 0.7 - - - -
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Residues in contact with LEU 212 (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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47A VAL* 3.6 25.6 - - + -
48A ILE 3.5 2.0 - - - -
49A ALA* 3.8 21.1 - - + -
67A VAL* 5.0 2.0 - - - -
190A ILE* 3.7 28.7 - - + +
193A ALA* 5.0 2.2 - - + -
194A LEU* 3.6 19.5 - - + -
197A LEU* 5.2 0.4 - - + -
210A ILE* 3.6 29.1 - - + -
211A GLU* 1.3 73.2 - - - +
213A ALA* 1.3 60.6 + - - +
214A ILE* 5.3 0.4 - - + -
223A LYS* 3.8 7.8 - - - +
224A LEU* 3.1 47.0 + - + +
229A ILE* 4.4 12.8 - - + +
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Residues in contact with ALA 213 (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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47A VAL* 3.6 3.6 - - - +
48A ILE* 2.9 38.5 + - + +
67A VAL* 3.4 29.8 - - + +
212A LEU* 1.3 74.4 - - - +
214A ILE* 1.3 65.0 + - - +
221A PHE* 3.8 19.7 - - + -
222A ARG 3.3 12.6 - - - +
223A LYS* 4.0 4.5 - - + -
224A LEU* 4.4 0.9 - - - +
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Residues in contact with ILE 214 (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 VAL 3.2 11.0 - - - +
47A VAL* 4.2 8.5 - - + -
186A LEU* 3.8 30.3 - - + -
190A ILE* 3.9 26.9 - - + -
213A ALA* 1.3 79.8 - - - +
215A ILE* 1.3 66.9 + - - +
216A GLY* 4.0 16.4 - - - +
217A ASP* 5.2 3.4 - - - +
220A ARG 4.8 0.7 - - - +
221A PHE* 3.4 5.7 - - - -
222A ARG* 2.8 64.6 + - + +
224A LEU* 4.3 16.6 - - + +
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Residues in contact with ILE 215 (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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45A GLY* 3.1 5.0 - - - -
46A VAL* 2.8 38.1 + - + +
48A ILE* 5.8 4.3 - - + -
73A ASP 3.7 8.1 - - - +
75A GLY* 3.6 6.3 - - - +
139A ALA* 3.5 40.6 - - + +
140A GLY 3.6 3.4 - - - +
141A HIS* 3.5 38.1 - - + +
147A PHE* 3.2 6.5 - - + -
214A ILE* 1.3 82.0 - - - +
216A GLY* 1.3 59.3 + - - +
220A ARG* 3.4 10.5 - - + -
221A PHE* 3.6 31.6 - - + -
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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