Contacts of the strand formed by residues 208 - 215 (chain A) in PDB entry 1N9P
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 LYS 208 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204A MSE 3.9 5.7 - - - +
205A ARG 2.9 24.8 + - - +
206A ASP* 3.8 10.1 - - + +
207A GLY* 1.3 88.5 - - - +
209A LEU* 1.3 60.6 + - - +
210A THR* 2.9 18.0 + - - +
273A VAL* 3.8 35.0 - - + -
274A ILE 4.5 11.4 + - - -
275A ASP* 5.3 5.9 - - - +
358A VAL* 5.3 5.0 - - - +
362A GLU* 5.1 8.3 + - - -
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Residues in contact with LEU 209 (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 ILE* 3.6 23.6 - - + -
203A SER* 3.7 22.0 - - - -
204A MSE 3.7 20.5 - - - +
208A LYS* 1.3 71.5 - - - +
210A THR* 1.3 59.5 + - - +
273A VAL* 4.2 0.7 - - - -
274A ILE* 3.3 33.3 + - + +
283A LEU 4.9 0.9 - - - +
323A TRP* 3.6 32.3 - - + -
353A THR* 4.1 12.8 - - + -
354A PRO 4.8 2.0 - - - +
356A TYR 3.8 11.4 - - - +
358A VAL* 4.0 28.1 - - + +
361A GLN* 4.6 11.5 + - - +
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Residues in contact with THR 210 (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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201A VAL 3.5 1.2 - - - +
202A ILE* 3.3 7.3 - - - -
203A SER 2.8 36.2 + - - +
205A ARG* 4.1 12.2 + - + +
208A LYS* 2.9 20.1 + - - +
209A LEU* 1.3 77.0 + - - +
211A LEU* 1.3 72.5 + - - +
212A MSE 3.5 17.4 - - + +
271A CYS* 3.6 27.8 - - + -
272A HIS 3.3 15.0 - - - +
273A VAL* 4.1 9.3 - - + +
274A ILE* 4.7 0.4 - - - -
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Residues in contact with LEU 211 (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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200A ALA* 4.1 19.5 - - + -
201A VAL 3.3 14.6 - - - +
202A ILE* 3.9 20.0 - - + -
210A THR* 1.3 70.8 - - - +
212A MSE 1.3 64.5 + - - +
213A PHE* 5.3 9.1 - - + -
230A CYS* 5.3 2.2 - - - -
251A LEU* 4.5 13.0 - - + -
270A ILE 3.6 0.7 - - - +
271A CYS* 3.6 0.7 - - - -
272A HIS* 2.8 59.6 + - + +
274A ILE* 4.4 7.8 - - + +
280A PHE* 3.8 27.8 - - + -
295A VAL* 4.6 11.9 - - + -
321A VAL* 4.3 10.8 - - + -
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Residues in contact with MSE 212 (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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200A ALA* 3.1 5.6 - - - +
201A VAL* 2.8 52.9 + - + -
203A SER* 3.2 36.6 - - - +
204A MSE 5.1 1.1 - - - +
205A ARG* 3.5 44.9 - - + +
210A THR* 3.5 30.7 - - + +
211A LEU* 1.3 80.7 - - - +
213A PHE* 1.3 64.4 + - - +
269A THR* 3.8 12.6 - - + -
270A ILE 3.2 12.8 - - - +
271A CYS* 3.8 4.9 - - - -
326A ARG* 5.7 4.0 - - + +
327A PHE* 3.6 5.2 - - + -
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Residues in contact with PHE 213 (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 PHE* 4.7 1.6 - + - -
197A SER* 3.7 2.9 - - - +
200A ALA* 4.2 6.1 - - + -
211A LEU* 5.3 10.1 - - + -
212A MSE 1.3 79.3 - - - +
214A ARG* 1.3 61.2 + - - +
215A VAL* 3.7 11.0 - - + -
228A ILE* 3.7 7.6 - - + -
230A CYS* 4.6 13.0 - - + -
253A VAL* 4.7 7.2 - - + -
269A THR* 3.6 2.5 - - - -
270A ILE* 2.8 66.6 + - + -
272A HIS* 6.2 2.0 - - + -
295A VAL* 5.4 2.2 - - + -
297A VAL* 3.6 39.7 - - + -
316A TYR* 3.5 41.1 - + + +
327A PHE* 3.6 9.9 - - - -
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Residues in contact with ARG 214 (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 PHE* 3.3 5.2 - - - +
197A SER* 2.8 45.6 + - - -
213A PHE* 1.3 77.0 - - - +
215A VAL* 1.3 68.2 + - - +
267A PRO* 3.8 21.8 - - - -
268A LEU 3.4 11.4 - - - +
269A THR* 4.1 13.6 + - - +
327A PHE* 3.5 35.0 - - + +
328A PHE 2.7 29.5 + - - -
329A PRO* 4.6 2.0 - - - +
330A VAL* 3.7 18.3 - - - +
344A GLN 3.1 21.4 + - - -
345A PHE* 2.9 40.3 + - + +
347A ALA 3.8 2.6 + - - -
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Residues in contact with VAL 215 (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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195A MSE 3.2 7.4 - - + +
196A PHE* 3.6 29.8 - - + -
213A PHE* 3.7 19.5 - - + -
214A ARG* 1.3 75.7 - - - +
216A GLY* 1.3 59.2 + - - +
228A ILE* 3.9 6.5 - - + -
262A LEU* 4.3 6.1 - - + -
264A LEU* 4.1 16.6 - - + -
266A SER 4.6 0.2 - - - +
267A PRO* 3.1 4.7 - - - +
268A LEU* 2.8 55.9 + - + +
270A ILE* 3.8 14.8 - - + -
299A LEU* 4.5 8.3 - - + -
345A PHE* 3.9 2.9 - - - -
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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