Contacts of the strand formed by residues 215 - 220 (chain A) in PDB entry 3C6M
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 MET 215 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A LYS 3.3 3.4 + - - +
193A ASP* 3.4 15.5 + - - +
194A VAL 2.7 32.7 + - - +
213A PRO 3.6 0.4 - - - -
214A LYS* 1.3 86.4 - - + +
216A VAL* 1.3 56.7 + - - +
217A THR* 4.2 10.5 + - - +
245A LYS* 6.1 2.2 - - - -
246A GLY 5.3 1.1 - - - +
247A ASP 5.0 3.1 - - - +
248A CYS* 3.2 28.5 - - - +
249A TYR* 3.6 8.7 - - - +
250A GLN* 3.5 47.8 - - + +
268A ARG* 4.6 10.3 - - - +
270A PHE* 5.7 0.5 - - - -
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Residues in contact with VAL 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 VAL* 3.3 17.5 - - + +
196A ILE* 3.6 30.7 - - + -
205A LEU* 4.0 12.3 - - + -
208A ILE* 3.4 32.3 - - + -
209A VAL* 4.8 4.0 - - + -
213A PRO* 3.6 20.0 - - + -
215A MET* 1.3 77.8 - - - +
217A THR* 1.3 64.6 + - - +
248A CYS 2.8 13.3 + - - +
249A TYR* 3.1 14.1 - - + +
250A GLN 3.0 25.1 + - - +
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Residues in contact with THR 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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194A VAL 2.7 13.6 + - - -
195A LEU* 3.4 19.0 - - + +
196A ILE* 2.7 33.6 + - - +
215A MET* 4.2 7.3 - - - +
216A VAL* 1.3 76.4 + - - +
218A MET* 1.3 55.5 + - - +
219A VAL* 4.2 10.5 - - + -
250A GLN* 3.1 33.0 + - + +
252A LEU* 4.4 6.7 - - + -
263A TYR* 3.6 22.4 - - - +
268A ARG* 4.3 6.8 + - - -
270A PHE* 4.9 6.1 - - - -
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Residues in contact with MET 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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196A ILE* 3.3 22.9 - - + -
198A GLY 3.1 19.1 - - - +
199A GLY* 3.3 34.3 - - - +
200A GLY* 4.3 0.9 - - - +
205A LEU* 4.1 28.7 - - + -
216A VAL 4.2 0.2 - - - -
217A THR* 1.3 74.1 - - - +
219A VAL* 1.3 62.2 + - - +
220A GLU* 4.2 4.3 - - + -
226A ILE* 3.9 17.5 - - + -
241A LEU* 4.5 7.4 - - + -
250A GLN 3.1 11.2 + - - +
251A VAL* 3.5 35.0 - - + +
252A LEU* 2.9 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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195A LEU* 4.0 22.0 - - + -
196A ILE 2.8 12.6 + - - +
197A LEU* 3.9 2.2 - - + -
198A GLY 3.0 22.3 + - - -
217A THR* 4.2 8.7 - - + -
218A MET* 1.3 76.9 - - - +
220A GLU* 1.3 57.5 + - - +
252A LEU* 3.6 12.8 - - + +
254A GLU* 3.2 22.0 - - + +
256A CYS* 3.6 25.2 - - + +
259A VAL* 3.8 33.0 - - + -
401A MTA 3.3 10.9 - - - -
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Residues in contact with GLU 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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198A GLY 3.6 11.2 - - - +
200A GLY* 2.9 19.8 + - - -
218A MET* 3.8 14.7 + - + -
219A VAL* 1.3 73.2 - - - +
221A ILE* 1.3 61.7 + - - +
222A ASP* 2.9 35.0 + - - +
223A GLN 4.9 0.2 - - - +
225A VAL* 4.7 0.2 - - - -
226A ILE* 4.1 21.1 - - + -
251A VAL* 4.9 0.7 - - + -
252A LEU 3.1 9.5 + - - +
253A ILE* 3.1 8.0 - - + +
254A GLU 3.1 18.2 + - - -
401A MTA 2.4 56.5 + - - +
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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