Contacts of the strand formed by residues 218 - 224 (chain B) in PDB entry 3NJ8
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 ARG 218 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A LEU* 3.7 22.9 - - + -
171B GLY* 4.6 13.0 + - - +
172B GLY 3.0 8.7 + - - +
173B SER* 3.2 20.3 + - - -
174B ALA 2.9 24.7 + - - -
216B GLY 5.2 1.8 - - - +
217B VAL* 1.3 73.0 - - - +
219B VAL* 1.3 64.5 + - - +
220B ASN* 3.4 8.6 - - - +
273B LEU 2.9 30.5 + - - -
274B LEU 4.1 1.2 - - - -
275B SER 3.3 22.4 + - - -
276B PRO* 5.3 0.6 - - - +
278B ALA* 2.9 24.4 + - - +
279B ARG* 3.3 25.6 - - - +
281B VAL 3.1 22.5 + - - +
282B SER* 3.5 6.5 - - - +
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Residues in contact with VAL 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B PHE* 4.0 31.6 - - + -
161B LEU* 4.3 6.7 - - + -
174B ALA* 3.4 11.7 - - + +
204B THR* 3.7 16.4 - - + +
207B LEU* 4.2 10.1 - - + -
208B ALA* 3.7 15.3 - - - +
211B ALA* 3.9 19.5 - - + -
217B VAL* 3.7 15.5 - - + +
218B ARG* 1.3 82.4 - - - +
220B ASN* 1.3 59.4 + - - +
282B SER* 3.1 7.3 + - - -
283B GLY* 2.7 35.0 + - - -
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Residues in contact with ASN 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B PHE* 4.8 0.9 - - - -
173B SER* 5.7 0.4 - - - -
174B ALA 2.9 9.7 + - - +
175B VAL* 3.2 8.6 - - + -
176B THR* 3.1 22.2 + - - +
204B THR* 3.3 11.8 - - - +
218B ARG* 3.4 16.0 - - - +
219B VAL* 1.3 78.5 - - - +
221B ALA* 1.3 59.2 + - - +
273B LEU* 4.2 27.2 + - + +
281B VAL* 2.7 32.7 + - - +
282B SER* 3.1 5.7 + - - +
283B GLY 3.1 7.6 + - - -
284B VAL* 2.9 35.1 + - + +
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Residues in contact with ALA 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B VAL* 4.7 1.3 - - - -
176B THR* 3.2 16.4 - - + +
178B SER* 5.0 4.0 - - - -
201B GLU* 4.9 9.0 - - + -
204B THR* 3.4 23.1 - - + +
220B ASN* 1.3 75.9 - - - +
222B ILE* 1.3 67.1 + - - +
223B SER 4.0 0.2 - - - -
273B LEU* 4.6 2.1 - - - +
284B VAL 2.7 16.5 + - - +
285B THR* 4.5 12.3 - - + +
286B LEU* 2.8 26.1 + - - +
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Residues in contact with ILE 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B VAL* 4.2 9.1 - - + +
176B THR 2.9 7.3 + - - -
177B LEU* 3.4 22.5 - - + +
178B SER* 2.8 26.7 + - - +
221B ALA* 1.3 71.4 - - - +
223B SER* 1.3 60.0 + - - +
224B ALA* 3.4 21.7 + - + -
266B VAL* 4.1 8.5 - - + +
269B ALA* 4.0 7.0 - - + -
270B ALA* 3.8 29.8 - - + +
273B LEU* 3.7 29.8 - - + -
286B LEU* 3.4 15.7 - - + +
288B VAL* 3.7 18.8 - - + -
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Residues in contact with SER 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B SER* 3.3 8.3 + - - -
179B TYR* 3.5 5.4 - - - -
180B LEU* 3.4 26.2 + - - +
183B GLU* 5.4 0.5 + - - +
201B GLU* 4.0 7.1 + - - -
221B ALA 4.0 2.0 - - - -
222B ILE* 1.3 70.3 - - - +
224B ALA* 1.3 59.2 + - - +
285B THR* 3.7 16.3 - - - +
286B LEU 3.2 6.1 + - - -
287B TYR* 3.2 37.4 - - - +
288B VAL 3.1 22.5 + - - +
289B ASP* 4.6 1.6 - - - +
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Residues in contact with ALA 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B TYR* 4.1 15.7 - - + +
177B LEU* 5.1 3.4 - - + -
178B SER 3.1 9.1 + - - +
179B TYR* 3.3 25.3 - - - -
180B LEU 4.9 0.2 + - - -
222B ILE* 3.4 19.9 + - + +
223B SER* 1.3 75.2 - - - +
225B GLY* 1.3 62.4 + - - +
266B VAL* 3.7 22.2 - - + -
288B VAL 3.3 5.2 - - - +
289B ASP* 4.3 3.8 - - - -
316B NAD 3.7 7.2 - - + -
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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