Contacts of the strand formed by residues 225 - 230 (chain A) in PDB entry 3NTV
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 225 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A THR* 3.9 29.6 - - + +
62A LEU* 3.7 30.5 - - + -
63A ILE* 4.5 11.7 - - + -
66A LEU* 5.6 0.4 - - + -
173A ILE* 3.6 22.2 - - + -
174A THR 3.4 18.2 - - - +
175A ASP* 4.0 9.4 - - + +
177A VAL* 3.5 5.0 - - - +
217A ASN 4.0 0.2 - - - +
218A PHE* 3.4 2.4 - - - -
219A LEU* 2.8 41.8 + - + +
221A ILE* 4.3 17.5 + - + -
224A GLY* 1.3 72.4 - - - -
226A ALA* 1.3 66.0 + - - +
227A ILE* 4.6 6.5 - - + -
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Residues in contact with ALA 226 (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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172A VAL 4.5 0.4 - - - -
173A ILE* 3.5 6.9 - - - +
174A THR* 2.8 39.5 + - - +
177A VAL* 4.0 10.5 - - + +
208A LEU* 4.3 5.8 - - + -
216A THR* 4.1 9.2 - - + -
217A ASN 3.2 7.2 - - - +
218A PHE* 3.7 30.3 - - + -
225A LEU* 1.3 74.7 - - - +
227A ILE* 1.3 65.4 + - - +
228A SER* 4.2 0.7 - - - +
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Residues in contact with ILE 227 (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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62A LEU* 4.4 13.2 - - + -
66A LEU* 3.7 21.5 - - + -
171A LEU* 4.6 4.7 - - + -
172A VAL 3.7 2.5 - - - -
173A ILE* 4.0 21.8 - - + -
216A THR* 3.2 1.1 - - - -
217A ASN* 2.9 42.3 + - - +
219A LEU* 4.5 6.3 - - + -
225A LEU* 4.6 9.2 - - + -
226A ALA* 1.3 78.3 - - - +
228A SER* 1.3 63.3 + - - +
229A ILE* 5.0 0.4 - - + -
62B LEU* 3.9 28.7 - - + -
65B GLN* 3.0 12.4 + - + +
69B MSE 3.4 28.5 - - + -
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Residues in contact with SER 228 (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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170A GLY 3.8 0.2 - - - +
171A LEU* 3.3 6.1 - - - -
172A VAL* 2.8 52.0 + - - +
174A THR* 5.3 0.9 + - - -
208A LEU* 3.7 17.8 - - - +
214A TYR* 4.0 19.7 - - - -
215A THR 3.3 4.9 - - - -
216A THR* 2.8 26.8 + - - +
226A ALA* 5.1 0.7 - - - +
227A ILE* 1.3 75.7 + - - +
229A ILE* 1.3 62.2 + - - +
230A LYS 3.9 0.3 + - - -
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Residues in contact with ILE 229 (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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169A GLN* 4.0 25.6 - - + +
170A GLY 3.6 3.4 - - - -
171A LEU* 3.8 16.4 - - + -
214A TYR* 3.3 5.5 - - - -
215A THR* 2.9 36.3 + - - +
228A SER* 1.3 71.5 - - - +
230A LYS* 1.3 74.4 + - - +
231A GLY* 3.5 1.5 + - - -
65B GLN* 3.4 30.3 - - - +
68B ARG* 3.7 28.5 - - + -
69B MSE 3.8 24.0 - - + +
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Residues in contact with LYS 230 (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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163A THR 2.9 21.4 + - - -
164A PRO* 4.1 8.9 + - - +
166A LEU* 2.8 37.9 + - + +
167A LYS 3.7 13.2 - - - +
168A HIS* 3.9 4.7 - - - +
169A GLN* 2.7 32.6 + - - +
170A GLY 2.9 17.7 + - - +
213A GLY 3.6 5.6 - - - +
214A TYR* 3.5 35.0 + - + +
228A SER 3.9 0.4 + - - -
229A ILE* 1.3 73.9 - - - +
231A GLY* 1.3 71.3 + - - +
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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