Contacts of the strand formed by residues 215 - 222 (chain A) in PDB entry 3REP
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 ASN 215 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211A ARG* 3.2 9.2 - - - +
212A TRP* 2.9 59.7 + - - +
213A GLN* 3.3 12.5 + - - +
214A GLY* 1.3 79.6 - - - +
216A ASP* 1.3 62.9 + - - +
217A ILE* 3.6 16.9 + - + +
254A LEU* 4.3 4.6 - - - +
270A HIS* 2.9 29.3 + - - +
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Residues in contact with ASP 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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196A LEU* 5.5 0.3 - - - +
209A LYS* 4.7 11.9 + - - +
210A GLY 3.8 4.5 - - - +
211A ARG* 2.6 38.1 + - - +
214A GLY 4.1 1.4 + - - -
215A ASN* 1.3 69.0 - - - +
217A ILE* 1.3 57.6 + - - +
270A HIS* 3.5 16.5 - - - -
271A TRP* 2.9 40.9 + - + +
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Residues in contact with ILE 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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193A LEU* 4.0 11.7 - - + -
194A ASN 5.6 0.2 - - - +
209A LYS* 3.5 8.5 - - - +
210A GLY* 2.9 46.3 + - - +
211A ARG* 3.7 6.7 - - - +
212A TRP* 3.7 24.9 - - + +
215A ASN* 3.7 24.0 - - + +
216A ASP* 1.3 79.2 - - - +
218A VAL* 1.3 66.9 + - - +
219A VAL* 3.6 24.0 - - + -
254A LEU* 4.0 15.9 - - + -
268A ILE* 4.0 13.9 - - + -
269A THR 3.1 14.1 - - - +
271A TRP* 3.7 5.2 - - - +
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Residues in contact with VAL 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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199A LEU* 3.8 18.6 - - + -
207A LEU* 3.9 20.4 - - + -
208A TRP 3.1 7.0 - - - +
209A LYS* 4.5 0.4 - - - -
217A ILE* 1.3 79.7 - - - +
219A VAL* 1.3 62.1 + - - +
220A LYS* 5.4 0.7 - - + +
267A LEU 4.0 0.3 - - - +
268A ILE* 3.4 6.9 - - - +
269A THR* 2.8 58.5 + - + +
271A TRP* 3.7 26.0 - - + +
338A ALA* 6.0 0.4 - - + -
502A ATP 3.6 26.5 - - + +
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Residues in contact with VAL 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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193A LEU* 4.0 11.7 - - + -
194A ASN 5.5 0.7 - - - +
195A PHE* 3.6 37.9 - - + -
206A GLU 3.6 1.4 - - - +
207A LEU* 3.3 7.1 - - - -
208A TRP* 2.8 38.8 + - + +
210A GLY* 4.8 7.4 - - - -
217A ILE* 3.6 26.7 - - + -
218A VAL* 1.3 75.6 - - - +
220A LYS* 1.3 58.5 + - - +
221A VAL* 3.7 4.3 + - + -
266A THR* 3.4 30.1 - - + -
267A LEU 3.5 3.8 - - - +
268A ILE* 4.3 1.8 - - + -
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Residues in contact with LYS 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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202A ASN* 4.4 2.0 + - - -
204A SER* 3.9 17.8 - - - -
206A GLU 3.5 13.4 + - - +
207A LEU* 3.8 17.4 - - + +
218A VAL* 4.0 1.4 - - + +
219A VAL* 1.3 72.2 - - - +
221A VAL* 1.3 60.5 + - - +
222A LEU* 3.8 21.1 - - + -
266A THR* 3.3 4.7 - - - -
267A LEU* 2.8 57.8 + - + +
338A ALA* 5.0 15.5 - - + +
345A GLN* 4.7 2.7 - - - -
501A MN 4.6 0.9 - - - -
502A ATP 2.7 64.9 + - - +
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Residues in contact with VAL 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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190A PHE* 5.2 3.6 - - + -
195A PHE* 4.2 15.5 - - + -
204A SER 3.8 0.3 - - - +
205A GLY* 3.2 5.7 - - - -
206A GLU* 2.8 54.9 + - + +
208A TRP* 4.3 13.9 - - + +
219A VAL* 4.0 20.0 - - + -
220A LYS* 1.3 74.2 - - - +
222A LEU* 1.3 62.1 + - - +
223A LYS* 6.3 0.4 - - + -
264A HIS* 3.7 36.8 - - + -
265A PRO 4.1 2.0 - - - -
266A THR* 4.2 9.4 - - + +
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Residues in contact with LEU 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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204A SER 3.4 11.4 - - - +
220A LYS* 3.8 26.7 - - + -
221A VAL* 1.3 72.1 - - - +
223A LYS* 1.3 60.0 - - - +
224A VAL* 3.9 8.1 + - + -
235A PHE* 3.9 12.8 - - + -
264A HIS* 3.7 20.2 + - - +
265A PRO* 2.9 32.1 + - + +
267A LEU* 3.7 20.0 - - + -
342A PHE* 3.6 29.6 - - + -
344A PHE* 4.3 11.2 - - + -
345A GLN* 3.8 26.7 - - + +
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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