Contacts of the strand formed by residues 208 - 217 (chain A) in PDB entry 6M85
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 MET* 3.3 9.0 - - - +
205A ARG 2.9 32.9 + - - +
206A ASP* 4.0 9.9 - - + +
207A GLY* 1.3 83.6 - - - +
209A LEU* 1.3 64.1 + - - +
210A CYS* 3.5 13.6 + - - -
273A GLU* 3.4 39.6 + - + +
274A ILE 6.0 0.9 - - - +
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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 VAL* 3.5 25.8 - - + -
203A ALA* 3.8 10.3 - - - +
204A MET* 3.7 24.1 - - + +
208A LYS* 1.3 71.8 - - - +
210A CYS* 1.3 59.6 + - - +
273A GLU* 4.0 0.2 - - - -
274A ILE* 3.0 39.8 + - + +
280A LEU 6.1 0.2 - - - +
283A ILE 5.2 0.4 - - - +
323A TRP* 3.8 32.1 - - + -
354A THR* 4.7 7.4 - - + -
355A PRO* 5.0 2.5 - - + +
357A CYS 4.1 4.9 - - - +
358A SER 4.4 0.2 - - - -
359A ALA* 4.0 33.7 - - + +
362A LEU* 4.4 13.2 - - + +
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Residues in contact with CYS 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 0.7 - - - +
202A VAL* 3.2 6.9 - - - -
203A ALA 2.9 34.2 + - - +
205A ARG* 4.6 10.3 - - + +
208A LYS* 3.6 19.5 - - - -
209A LEU* 1.3 78.6 - - - +
211A LEU* 1.3 59.8 + - - +
212A MET* 3.9 19.1 + - + +
271A LEU* 4.4 15.9 - - + -
272A HIS 3.3 7.9 - - - +
273A GLU* 4.0 27.6 - - - -
274A ILE* 4.0 5.4 - - - -
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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 10.3 - - + -
201A VAL 3.4 14.1 - - - +
202A VAL* 4.1 6.5 - - + -
210A CYS* 1.3 72.7 - - - +
212A MET* 1.3 63.6 + - - +
213A TRP* 4.1 24.3 - - + -
251A ILE* 4.6 6.3 - - + -
270A ILE 3.7 0.7 - - - +
272A HIS* 2.9 53.2 + - + +
274A ILE* 3.8 10.0 - - + +
280A LEU* 3.7 14.8 - - + -
295A ILE* 3.3 34.3 - - + -
321A ILE* 3.9 24.5 - - + -
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Residues in contact with MET 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* 3.2 5.2 - - - -
201A VAL* 2.8 62.7 + - + +
203A ALA* 4.1 13.2 - - + +
204A MET 5.9 0.7 - - - +
205A ARG* 3.9 25.1 - - + +
210A CYS* 4.1 13.9 - - + +
211A LEU* 1.3 81.1 - - - +
213A TRP* 1.3 62.4 + - - +
269A THR* 3.8 13.0 - - + -
270A ILE 3.2 8.5 - - - +
271A LEU* 3.4 31.0 - - + -
326A ARG* 4.1 24.0 - - + -
327A PHE* 3.6 7.8 - - + +
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Residues in contact with TRP 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* 4.3 7.0 - + - -
200A ALA* 4.4 4.5 - - + +
211A LEU* 4.1 36.1 - - + -
212A MET* 1.3 79.7 - - - +
214A ARG* 1.3 58.5 + - - +
215A VAL* 4.2 15.3 - - + +
228A VAL* 5.4 3.9 - - + +
229A ARG 4.3 5.5 + - - -
230A ALA* 3.5 27.8 - - + -
251A ILE* 4.6 0.2 - - + -
253A VAL* 3.4 25.4 - - + -
269A THR* 3.5 2.0 - - - -
270A ILE* 2.7 66.5 + - + +
272A HIS* 4.3 6.5 - - + -
295A ILE* 5.4 1.3 - - + -
297A VAL* 3.5 28.8 - - + +
298A ILE 5.5 0.6 + - - +
316A TYR* 3.5 29.4 - + + +
327A PHE* 3.9 10.3 - - - -
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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* 3.5 5.9 - - - +
197A SER* 3.1 41.4 + - - +
213A TRP* 1.3 75.0 - - - +
215A VAL* 1.3 68.0 + - - +
267A PRO* 4.1 12.1 + - + +
268A ILE 3.4 12.1 + - - +
269A THR* 4.0 14.0 + - - +
316A TYR* 4.6 0.2 + - - -
327A PHE* 3.7 30.2 + - + +
328A GLU 2.8 33.1 + - - -
329A PRO* 4.0 8.3 - - - +
330A VAL* 3.6 13.7 - - - +
344A HIS 3.2 8.1 + - - -
345A PHE* 2.8 65.0 + - + +
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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 LEU 3.3 5.8 - - - +
196A PHE* 3.4 40.4 - - + -
213A TRP* 4.2 10.3 - - + +
214A ARG* 1.3 73.9 - - - +
216A GLY* 1.3 59.7 + - - +
228A VAL* 5.0 2.5 - - + -
262A ILE* 4.3 17.9 - - + -
264A LEU* 3.7 8.1 - - + +
267A PRO* 3.3 2.3 - - - +
268A ILE* 2.9 39.5 + - + +
270A ILE* 4.0 22.2 - - + -
299A LEU* 4.2 17.9 - - + -
345A PHE* 4.0 3.8 - - - -
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Residues in contact with GLY 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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194A LEU* 3.7 5.5 - - - +
195A LEU* 2.9 37.5 + - - +
215A VAL* 1.3 76.6 - - - +
217A ASN* 1.3 61.1 + - - -
264A LEU* 4.1 8.1 - - - -
267A PRO* 4.1 10.3 - - - -
342A TYR* 4.2 4.7 - - - -
345A PHE* 3.7 16.6 - - - -
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Residues in contact with ASN 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 THR* 3.4 17.8 + - - +
194A LEU* 4.3 2.2 - - + -
216A GLY* 1.3 72.3 - - - -
218A LEU* 1.3 64.7 + - - +
219A ARG* 3.3 20.7 + - - +
221A SER 2.8 28.2 + - - +
222A HIS* 4.2 2.4 + - - +
223A ILE* 4.1 23.2 - - - +
264A LEU* 4.0 32.5 + - + +
265A VAL 4.5 10.1 + - - +
267A PRO* 5.4 0.4 - - - +
342A TYR* 2.8 24.5 + - - -
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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