Contacts of the strand formed by residues 214 - 218 (chain B) in PDB entry 1R9T
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 ALA 214 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46B GLN* 5.5 0.7 - - - +
47B GLN* 4.9 0.6 - - - +
212B LEU 3.1 6.5 + - - -
213B ILE* 1.3 85.7 - - - +
215B GLN* 1.3 68.3 + - - +
406B LEU* 4.9 10.3 - - + -
407B ASP 3.5 1.1 - - - -
408B LEU* 3.3 29.4 - - + +
497B ARG 3.0 25.1 + - - +
498B THR* 3.3 15.5 - - - +
499B ASN 3.4 6.8 + - - -
539B LEU* 6.0 0.9 - - + -
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Residues in contact with GLN 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B ILE* 2.9 19.9 - - - +
214B ALA* 1.3 81.8 - - - +
216B GLU* 1.3 64.2 + - - +
217B ARG* 3.9 1.5 + - + +
405B ARG 3.4 0.3 - - - +
406B LEU* 2.8 7.2 - - - -
407B ASP* 2.4 53.5 + - + +
412B LEU* 5.1 8.1 - - + -
475B SER 4.4 8.1 + - - -
477B ALA* 3.3 23.5 - - - +
479B VAL* 3.1 18.7 - - + +
499B ASN* 3.4 24.7 + - - +
501B PRO* 5.3 9.9 - - + +
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Residues in contact with GLU 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B GLN* 1.3 76.1 - - - +
217B ARG* 1.3 71.9 + - - +
401B PHE* 3.6 15.8 - - + -
404B LYS* 3.5 28.8 + - + +
405B ARG 3.2 9.4 - - - +
406B LEU* 3.7 13.2 - - + -
498B THR* 3.9 7.4 - - + +
499B ASN 2.9 8.7 + - - +
500B THR* 2.2 46.1 + - + +
501B PRO* 3.6 22.2 - - - +
518B HIS* 5.7 0.2 - - - -
537B LYS* 2.5 26.2 + - - +
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Residues in contact with ARG 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B GLN* 4.9 2.0 - - + +
216B GLU* 1.3 82.5 - - - +
218B SER* 1.3 80.6 + - - +
220B GLY 4.5 10.1 - - - +
241B ARG* 4.4 18.4 - - - +
249B ARG* 5.9 4.6 - - - +
404B LYS* 3.0 13.9 - - - +
405B ARG* 2.7 71.8 + - - +
407B ASP* 3.0 47.5 + - + +
501B PRO* 6.3 0.7 - - + -
629B ASP* 3.9 14.1 + - - -
630B ALA 4.3 3.0 + - - -
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Residues in contact with SER 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B ARG* 1.3 90.1 + - - +
219B ALA* 1.4 74.3 + - - +
224B GLN* 5.2 5.2 + - - -
241B ARG* 4.3 25.2 + - - +
398B ARG* 5.3 2.4 + - - +
403B LYS 4.0 5.3 + - - -
404B LYS* 3.9 21.1 + - - +
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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