Contacts of the strand formed by residues 211 - 216 (chain C) in PDB entry 3GUT
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 GLU 211 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200C ASN* 4.7 5.4 + - - +
201C ARG* 4.3 10.5 + - - +
209C GLY 3.5 2.6 + - - -
210C ASP* 1.3 71.0 - - - +
212C ILE* 1.3 72.9 + - - +
213C PHE* 3.8 20.2 + - + -
251C VAL* 3.9 23.4 - - + +
252C PHE 3.8 4.9 - - - +
253C ARG* 3.2 38.7 + - - +
552D ARG* 3.8 18.5 + - - -
553D MET 5.5 0.7 - - - +
554D ASP* 5.2 5.0 - - - +
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Residues in contact with ILE 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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199C VAL* 4.0 15.5 - - + -
200C ASN* 3.9 2.2 - - - +
201C ARG* 3.3 54.5 - - + +
210C ASP* 3.5 15.9 - - + +
211C GLU* 1.3 92.8 - - - +
213C PHE* 1.3 65.9 + - - +
214C LEU* 4.9 0.7 - - + -
250C ILE 3.4 0.7 - - - +
251C VAL* 3.3 5.8 - - - -
252C PHE* 2.8 62.1 + - + +
254C THR* 4.1 16.2 - - + -
270C MET* 5.6 2.7 - - - -
286C PHE* 4.8 6.1 - - + -
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Residues in contact with PHE 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 VAL* 3.5 4.3 - - - -
200C ASN* 2.8 42.9 + - - +
211C GLU* 3.8 24.0 - - + -
212C ILE* 1.3 75.3 - - - +
214C LEU* 1.3 59.8 + - - +
215C LEU* 4.2 2.0 - - + -
250C ILE 3.9 2.7 - - - -
251C VAL* 3.6 26.5 - - + -
552D ARG* 3.5 28.0 - - + -
553D MET* 3.6 2.2 - - - -
554D ASP* 3.2 45.5 - - + -
567D TYR* 3.4 38.7 - + + -
569D LEU* 4.5 15.7 - - + -
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Residues in contact with LEU 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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196C ILE* 4.1 20.0 - - + -
198C ARG 3.9 3.8 - - - -
199C VAL* 4.2 11.9 - - + -
212C ILE* 4.9 0.7 - - + -
213C PHE* 1.3 74.8 - - - +
215C LEU* 1.3 64.1 + - - +
216C CYS* 3.5 27.1 - - + -
226C VAL* 4.6 8.3 - - + -
249C ALA* 3.0 4.2 - - - +
250C ILE* 2.7 59.0 + - + +
252C PHE* 4.0 27.1 - - + -
270C MET* 5.7 4.9 - - + -
272C LEU* 3.9 26.0 - - + -
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Residues in contact with LEU 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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196C ILE* 4.0 0.3 - - - +
197C CYS 3.1 20.2 + - - -
198C ARG* 3.4 25.2 + - + +
213C PHE* 5.2 1.6 - - + -
214C LEU* 1.3 81.0 - - - +
216C CYS* 1.3 62.0 + - - +
248C VAL 3.4 2.7 - - - -
249C ALA* 3.5 24.5 - - + -
567D TYR* 4.0 33.2 - - + -
569D LEU* 4.2 12.1 - - + -
604D HIS* 3.3 42.4 - - + +
608D ALA* 4.2 7.2 - - + -
610D VAL* 4.0 16.4 - - + -
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Residues in contact with CYS 216 (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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195C LYS 3.4 16.8 - - - +
196C ILE* 4.5 0.2 - - - -
197C CYS* 4.0 6.7 - - - -
214C LEU* 3.5 22.7 - - + -
215C LEU* 1.3 77.7 - - - +
217C ASP* 1.3 74.2 + - - +
219C VAL* 4.7 6.7 - - + -
247C GLN 4.7 0.9 - - - -
248C VAL* 3.0 30.9 + - - +
249C ALA 3.7 3.8 - - - -
250C ILE* 4.0 13.0 - - - -
272C LEU* 4.2 9.4 - - + -
604D HIS* 2.9 21.8 + - - -
605D ARG* 4.2 3.3 - - - +
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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