Contacts of the strand formed by residues 215 - 223 (chain A) in PDB entry 5NV6
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 ALA 215 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A THR* 3.5 1.0 - - - -
212A VAL* 2.8 41.3 + - - +
213A ASN 3.2 0.8 - - - +
214A CYS* 1.3 75.4 - - - +
216A ARG* 1.3 65.9 + - - +
217A LEU 3.5 0.9 + - - -
232A ILE* 4.3 5.8 - - + +
233A ASP* 4.2 7.0 - - - +
234A LYS* 3.5 41.1 - - + +
236A ILE* 3.9 12.3 - - + -
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Residues in contact with ARG 216 (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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59A ARG* 3.6 25.1 - - - +
60A LYS 2.9 29.9 + - - +
61A TYR* 3.6 40.0 + - - +
62A PHE 5.1 0.8 - - - +
209A ILE* 4.0 23.8 - - + -
210A VAL 3.8 4.7 - - - -
211A THR* 4.3 4.3 - - - -
214A CYS 3.7 4.8 + - - -
215A ALA* 1.3 69.2 - - - +
217A LEU* 1.3 70.8 + - - +
218A LEU* 3.2 31.3 + - - +
232A ILE* 3.6 0.3 - - - -
233A ASP* 3.0 40.1 + - + +
319A GLU* 3.3 36.5 + - + +
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Residues in contact with LEU 217 (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 PHE 5.7 0.2 - - - +
141A PHE* 4.7 1.8 - - + -
182A THR* 4.5 6.3 - - + -
185A LEU* 4.2 14.6 - - + -
210A VAL* 2.9 47.9 + - + +
212A VAL* 4.6 8.7 - - + -
215A ALA 3.5 1.4 + - - -
216A ARG* 1.3 77.8 + - - +
218A LEU* 1.3 65.9 + - - +
219A LYS 3.8 11.9 - - - +
220A ALA* 3.7 21.1 - - + -
230A HIS* 3.5 33.2 - - + -
231A LEU 3.9 1.6 - - - +
232A ILE* 4.0 17.3 - - + -
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Residues in contact with LEU 218 (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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60A LYS 4.4 1.3 - - - +
62A PHE* 3.2 50.4 + - + +
144A SER* 4.1 10.1 - - - +
216A ARG* 3.5 45.1 - - - +
217A LEU* 1.3 75.5 - - - +
219A LYS* 1.3 59.1 + - - +
220A ALA* 4.2 1.4 + - - +
231A LEU* 2.8 31.6 + - + +
232A ILE 3.7 24.2 - - - +
233A ASP* 3.7 18.2 - - - +
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Residues in contact with LYS 219 (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 PHE* 3.7 41.1 - - + -
83A GLU* 4.6 9.3 + - - -
112A VAL 5.2 1.0 + - - -
113A VAL* 3.1 34.5 + - + +
217A LEU* 3.8 4.0 - - - +
218A LEU* 1.3 79.3 - - - +
220A ALA* 1.3 61.2 + - - +
222A HIS* 3.7 25.1 - - + +
230A HIS* 3.6 2.3 - - - -
231A LEU* 2.9 48.3 + - + +
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Residues in contact with ALA 220 (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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86A PRO* 3.8 10.4 - - - +
182A THR* 3.7 26.0 - - + -
217A LEU* 3.7 18.2 - - + -
218A LEU 4.2 1.3 + - - +
219A LYS* 1.3 76.7 - - - +
221A ASP* 1.3 70.0 + - - +
222A HIS* 3.1 15.8 + - - -
229A VAL 4.7 0.4 - - - -
230A HIS* 4.1 6.3 - - + -
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Residues in contact with ASP 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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86A PRO* 3.6 16.9 - - + +
181A LEU* 3.4 24.7 - - + +
182A THR* 2.7 51.4 + - - +
220A ALA* 1.3 73.1 - - - +
222A HIS* 1.3 59.1 + - - +
223A HIS* 3.4 23.1 + - + -
228A VAL* 3.9 10.3 - - - -
229A VAL 4.1 0.4 + - - -
230A HIS* 3.6 13.3 + - - -
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Residues in contact with HIS 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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86A PRO* 3.6 28.8 - - + +
87A GLY 4.7 4.0 - - - -
109A THR* 3.7 12.6 - - + +
112A VAL* 5.6 7.4 - - + -
113A VAL* 3.6 30.2 - - + +
219A LYS* 3.7 33.2 - - + +
220A ALA 3.1 33.4 + - - -
221A ASP* 1.3 71.9 - - - +
223A HIS* 1.3 64.4 + - - +
224A ALA 3.6 0.7 + - - -
228A VAL* 4.0 2.1 - - - +
229A VAL* 2.9 37.9 + - - +
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Residues in contact with HIS 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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103A LEU* 4.0 26.8 - - + +
104A SER 4.8 0.5 + - - +
109A THR* 4.3 7.1 + - - +
179A ARG* 4.2 17.5 + - - -
181A LEU* 3.5 27.9 - - + +
221A ASP* 3.4 21.4 + - + -
222A HIS* 1.3 73.0 - - - +
224A ALA* 1.3 60.0 + - - +
227A GLY 3.8 3.8 - - - +
228A VAL* 3.6 18.4 - - + -
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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