Contacts of the strand formed by residues 183 - 193 (chain A) in PDB entry 3NVN
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 183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A THR* 3.6 28.5 - - + -
178A ILE 3.5 4.9 - - - +
179A ASP* 3.7 22.4 - - - +
182A ARG* 1.3 74.5 - - - +
184A VAL* 1.3 60.8 + - - +
185A LYS* 4.4 8.4 + - + +
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Residues in contact with VAL 184 (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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176A ASP 3.6 0.9 - - - +
177A THR* 3.5 1.9 - - - -
178A ILE* 2.8 65.1 + - + +
182A ARG* 4.0 21.3 - - + +
183A ILE* 1.3 79.2 - - - +
185A LYS* 1.3 65.0 - - - +
186A ILE* 4.6 10.5 - - + -
226A ARG* 5.1 6.5 - - - +
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Residues in contact with LYS 185 (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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175A THR* 3.8 11.0 - - + -
176A ASP 3.2 3.8 - - - -
177A THR* 3.8 26.8 + - + +
183A ILE* 4.4 7.2 + - + +
184A VAL* 1.3 74.0 - - - +
186A ILE* 1.3 61.4 + - - +
226A ARG* 3.0 47.7 + - + +
227A GLN* 3.3 35.4 - - + +
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Residues in contact with ILE 186 (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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175A THR* 3.3 4.1 - - - +
176A ASP 2.7 38.5 + - - +
178A ILE* 3.6 23.6 - - + -
184A VAL* 4.5 11.4 - - + +
185A LYS* 1.3 80.9 - - - +
187A PRO* 1.3 68.0 - - + +
188A TYR* 3.4 31.1 - - + +
215A GLU* 3.2 46.4 - - + +
226A ARG* 4.4 8.3 - - - +
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Residues in contact with PRO 187 (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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174A PHE 3.6 5.2 - - - +
175A THR* 4.2 1.1 - - - +
186A ILE* 1.3 90.5 - - + +
188A TYR* 1.3 63.4 + - - +
215A GLU* 3.5 4.3 - - + +
216A LEU* 3.1 49.1 + - + +
217A GLU* 5.5 0.2 - - - -
225A TYR 4.1 11.9 - - - +
226A ARG* 3.4 39.0 - - - +
228A ILE* 3.9 17.7 - - + -
246A PHE* 4.0 9.6 - - + -
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Residues in contact with TYR 188 (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 ILE 4.4 0.2 - - - -
173A LEU* 3.4 7.6 - - - +
174A PHE* 2.9 62.1 + + + +
176A ASP* 3.5 26.8 + - + -
178A ILE* 4.6 5.2 - - - +
186A ILE* 3.4 50.6 - - + +
187A PRO* 1.3 74.4 - - - +
189A ILE* 1.3 60.9 + - - +
190A ALA 4.3 0.2 - - - -
213A LYS* 3.7 26.1 + - + -
214A VAL 3.3 24.0 - - - +
215A GLU* 3.8 5.3 + - + -
216A LEU* 4.1 8.6 - - - +
228A ILE* 4.2 0.5 - - - +
307A GLU* 3.5 37.1 + - + -
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Residues in contact with ILE 189 (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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160A PHE* 4.8 0.7 - - + -
171A TYR* 3.9 31.0 - - + -
172A ILE 3.2 18.6 - - - +
173A LEU* 3.8 18.8 - - + -
188A TYR* 1.3 74.1 - - - +
190A ALA* 1.3 63.2 + - - +
213A LYS* 3.3 1.7 - - - -
214A VAL* 3.0 44.4 + - + +
216A LEU* 3.9 26.0 - - + -
242A LEU* 4.5 9.0 - - + -
260A MET* 5.5 0.7 - - + -
263A ILE* 4.6 22.9 - - + -
267A PHE* 3.4 6.6 - - + -
312A ILE* 5.2 0.9 - - + -
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Residues in contact with ALA 190 (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 VAL 3.6 0.3 - - - +
171A TYR* 3.2 9.6 - - - +
172A ILE* 2.8 42.7 + - + -
174A PHE* 4.1 4.7 - - + -
188A TYR 4.3 0.2 - - - -
189A ILE* 1.3 75.5 - - - +
191A GLN* 1.3 60.6 + - - +
192A MET* 4.3 1.3 - - - -
211A PHE* 3.4 33.4 - - + -
212A LEU 3.0 12.8 - - - +
213A LYS* 3.8 7.2 - - + -
267A PHE* 4.1 1.6 - - - -
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Residues in contact with GLN 191 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A LYS* 2.8 31.3 + - + +
170A VAL 3.4 6.1 - - - -
171A TYR* 3.3 28.7 + - + -
190A ALA* 1.3 73.4 - - - +
192A MET* 1.3 68.7 + - - +
210A THR* 2.9 29.1 + - - +
211A PHE* 3.2 4.3 - - - -
212A LEU* 2.8 34.4 + - + +
267A PHE* 3.5 46.1 - - + +
285A GLY* 3.4 19.8 + - - +
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Residues in contact with MET 192 (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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133A TRP* 3.4 29.8 - - + +
169A LYS* 3.2 9.4 - - - +
170A VAL* 2.8 53.8 + - + +
172A ILE* 3.8 35.4 - - + -
190A ALA 4.2 1.3 - - - +
191A GLN* 1.3 86.9 - - - +
193A CYS* 1.3 59.8 + - - +
208A TRP* 3.8 35.9 - - + -
210A THR* 3.6 13.0 - - - +
211A PHE* 3.9 22.9 - - + -
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Residues in contact with CYS 193 (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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168A ASP 3.8 6.1 - - - +
169A LYS* 3.8 7.0 - - - -
192A MET* 1.3 71.3 - - - +
194A LEU* 1.3 66.0 + - - +
195A ASN 4.4 2.7 - - - +
196A ASP* 3.2 22.9 + - + +
208A TRP* 3.3 17.4 - - - -
210A THR* 3.0 31.0 + - + +
286A ILE 4.2 0.4 - - - -
287A CYS* 2.0 60.8 - - + -
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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