Contacts of the helix formed by residues 211 - 215 (chain C) in PDB entry 1ML3
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 TRP 211 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B ASP* 4.5 10.8 + - - -
44B GLU* 4.1 11.4 - - + -
45B TYR* 3.2 61.8 + + + +
48B TYR* 3.6 46.8 + + + -
207C SER 3.7 5.2 - - - -
208C VAL* 3.6 24.3 + - - +
210C ASP* 1.3 71.3 + - - +
212C ARG* 1.3 55.1 + - - +
214C GLY* 2.8 25.5 + - - -
215C ARG* 3.7 8.3 + - - +
295D GLU* 3.7 34.2 + - + +
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Residues in contact with ARG 212 (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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210C ASP* 3.4 7.1 - - - +
211C TRP* 1.3 76.4 - - - +
213C GLY* 1.3 58.0 + - - +
214C GLY 2.9 5.7 + - - -
215C ARG* 3.1 18.4 + - - +
222C ILE* 3.3 27.7 - - + +
223C PRO* 3.6 36.3 + - - +
294D GLU 4.0 3.6 + - - -
295D GLU* 3.1 37.7 + - + +
296D LEU* 2.8 44.6 + - - +
297D VAL* 4.2 7.4 - - + -
311D ASP* 2.8 40.2 + - - -
313D LYS* 3.6 13.5 - - - +
314D ALA* 3.5 18.0 - - - +
317D GLN* 5.2 2.2 + - - -
332D TRP* 4.6 0.2 - - - +
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Residues in contact with GLY 213 (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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199C THR 4.7 2.8 - - - +
200C GLN* 4.2 28.6 - - - +
201C LYS* 4.4 3.8 + - - +
207C SER* 4.1 6.0 + - - -
210C ASP* 3.1 31.3 + - - -
212C ARG* 1.3 78.0 - - - +
214C GLY* 1.3 58.1 + - - +
215C ARG 3.5 2.7 - - - +
222C ILE* 4.1 8.7 - - - +
249C ARG* 6.6 0.4 - - - -
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Residues in contact with GLY 214 (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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45B TYR* 5.1 0.4 - - - -
201C LYS* 3.8 9.5 - - - +
204C ASP* 3.5 0.2 - - - -
205C GLY* 2.7 46.6 + - - +
206C VAL 5.1 0.2 - - - -
207C SER* 3.6 12.8 - - - -
210C ASP 3.3 2.0 + - - -
211C TRP 2.8 13.5 + - - -
213C GLY* 1.3 79.3 - - - +
215C ARG* 1.3 63.0 + - - +
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Residues in contact with ARG 215 (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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48B TYR* 3.0 36.6 + - - +
49B GLN* 6.6 0.2 - - - +
52B TYR* 3.9 14.1 + - - +
53B ASP 3.5 7.3 - - - +
54B THR* 3.2 34.3 - - + +
200C GLN* 5.1 0.5 - - - +
201C LYS 3.8 6.0 + - - +
204C ASP* 3.0 24.5 + - - -
211C TRP 4.0 2.2 - - - +
212C ARG 3.1 14.7 + - - +
213C GLY 4.5 2.8 - - - +
214C GLY* 1.3 82.5 - - - +
216C ALA* 1.3 66.6 + - - +
217C ALA* 3.0 4.9 + - - +
220C ASN* 4.3 0.7 - - - +
222C ILE* 3.5 11.8 - - + +
297D VAL* 3.5 25.2 - - + +
299D ALA* 4.9 0.2 - - - +
300D ASP* 2.8 43.6 + - - -
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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