Contacts of the strand formed by residues 215 - 219 (chain C) in PDB entry 3M0V
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 215 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C LYS 3.2 7.1 + - - +
175C ALA* 3.1 7.3 - - + +
176C LEU 2.9 25.1 + - - -
210C LEU* 4.3 7.5 - - - +
213C ASP 5.6 1.3 - - - +
214C TRP* 1.3 78.3 - - - +
216C LEU* 1.3 61.2 + - - +
217C PHE* 3.8 27.1 - - + -
248C LYS* 3.2 18.2 - - + +
250C GLN* 2.7 37.8 + - - +
277C LEU 5.4 0.8 + - - -
278C GLY 5.2 2.4 + - - -
321C HIS* 4.8 14.6 + - - +
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Residues in contact with LEU 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C LEU* 3.4 29.2 - - + +
178C VAL* 3.8 22.0 - - + -
203C MET* 3.7 38.8 - - + +
206C ILE* 4.1 9.2 - - + -
207C TYR* 4.4 10.3 - - + +
210C LEU* 3.5 25.3 - - + +
215C LYS* 1.3 72.5 - - - +
217C PHE* 1.3 60.7 + - - +
218C SER* 3.9 0.9 + - - +
245C LEU* 4.0 17.5 - - + -
248C LYS 2.8 10.4 + - - +
249C ALA* 3.4 5.2 - - - +
250C GLN 3.0 25.3 + - - +
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Residues in contact with PHE 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C ALA* 4.5 4.7 - - + -
175C ALA* 3.7 24.7 - - + -
176C LEU 2.7 9.8 + - - -
177C THR* 3.3 25.2 - - - +
178C VAL* 2.7 33.9 + - - +
215C LYS* 3.8 34.3 - - + -
216C LEU* 1.3 77.7 - - - +
218C SER* 1.3 57.6 + - - +
219C GLU 3.9 0.2 + - - -
250C GLN* 3.4 9.9 - - + -
251C CYS 5.1 0.2 - - - -
252C LEU* 4.0 24.2 - - + -
278C GLY* 3.3 41.7 - - - -
279C GLY 4.8 0.2 - - - -
323C ALA* 4.1 21.8 - - + -
325C MET* 4.6 0.7 - - + -
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Residues in contact with SER 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C VAL* 3.7 7.0 - - - -
199C TYR* 3.6 24.5 - - - -
203C MET* 4.3 7.0 - - - -
216C LEU 3.9 1.6 + - - -
217C PHE* 1.3 73.4 - - - +
219C GLU* 1.3 59.0 + - - +
232C VAL* 5.1 1.6 - - - -
238C ASN* 2.6 44.2 + - - -
241C ILE* 3.9 18.7 - - - +
242C ALA* 4.9 2.1 + - - +
245C LEU* 5.8 0.2 - - - +
249C ALA* 6.1 0.7 - - - +
250C GLN 3.2 10.8 + - - -
252C LEU 3.0 13.1 + - - -
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Residues in contact with GLU 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177C THR* 4.1 8.2 - - + +
178C VAL 3.2 16.1 + - - +
179C TRP* 3.3 29.6 - - + +
180C ILE 5.2 0.3 + - - -
217C PHE 3.9 0.2 + - - -
218C SER* 1.3 72.3 - - - +
220C HIS* 1.3 72.1 + - - +
221C LYS 4.0 0.2 + - - -
232C VAL* 4.0 10.2 - - - +
252C LEU* 3.8 23.1 - - + +
254C ASP* 3.1 6.2 - - + +
257C HIS* 3.1 16.5 - - + +
281C HIS* 2.9 14.8 + - - -
505C MN 2.2 30.4 + - - -
2003C RNS 2.8 19.1 + - - -
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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