Contacts of the strand formed by residues 220 - 225 (chain B) in PDB entry 3RU0
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 HIS 220 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32B ARG* 2.9 46.0 + - + +
33B SER* 3.6 25.1 + - - -
34B ASP* 2.7 29.6 + - - +
215B VAL 3.8 0.2 - - - +
216B PHE* 3.2 4.8 - - - -
217B ASN* 2.8 47.1 + - + +
218B GLY 3.2 1.2 - - - -
219B PRO* 1.3 79.1 - - + +
221B LEU* 1.3 58.9 + - - +
222B LEU* 3.6 22.4 - - + +
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Residues in contact with LEU 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B PHE 5.0 0.2 - - - +
32B ARG* 3.2 6.8 - - - +
33B SER 2.9 35.2 + - - +
183B PHE* 4.1 4.5 - - + -
198B TYR* 3.7 32.3 - - + -
201B ILE* 3.7 42.0 - - + -
214B ILE* 4.0 24.0 - - + -
215B VAL 3.6 4.0 - - - +
216B PHE* 3.8 28.9 - - + -
219B PRO 3.6 0.2 + - - -
220B HIS* 1.3 75.4 + - - +
222B LEU* 1.3 79.3 + - - +
223B LEU* 3.8 2.5 - - + +
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Residues in contact with LEU 222 (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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29B LEU* 4.3 12.8 - - + -
31B PHE 3.8 1.8 - - - -
32B ARG* 3.6 29.6 - - + +
213B SER 3.8 0.7 - - - +
214B ILE* 3.2 5.9 - - - +
215B VAL* 2.9 46.4 + - + +
217B ASN* 5.6 3.6 - - + -
220B HIS* 3.6 28.5 - - + +
221B LEU* 1.3 77.1 - - - +
223B LEU* 1.3 59.7 + - - +
224B ARG* 3.9 14.7 + - - +
404B HIS 3.8 22.2 - - - +
407B GLU* 3.9 20.2 - - + +
408B HIS* 4.1 8.5 - - + +
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Residues in contact with LEU 223 (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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6B VAL* 5.2 0.2 - - + -
18B LEU* 4.2 17.9 - - + -
29B LEU* 3.5 4.5 - - - +
30B LEU* 2.8 48.7 + - + -
31B PHE* 2.9 33.4 + - + +
201B ILE* 4.7 6.1 - - + -
204B LEU* 3.5 36.1 - - + -
212B CYS* 3.9 24.2 - - + -
213B SER 3.7 4.5 - - - +
214B ILE* 3.7 18.4 - - + -
221B LEU* 3.8 6.4 - - + +
222B LEU* 1.3 71.4 - - - +
224B ARG* 1.3 60.3 + - - +
235B LEU* 5.2 0.2 - - + -
237B ILE* 4.0 1.3 - - + -
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Residues in contact with ARG 224 (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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27B GLY 2.9 20.7 + - - +
28B GLU 3.3 8.5 - - - +
29B LEU* 3.8 22.3 - - + +
30B LEU* 4.1 5.6 - - - -
212B CYS* 3.3 4.0 - - - +
213B SER* 2.9 37.0 + - - +
222B LEU* 3.9 12.8 - - + +
223B LEU* 1.3 79.9 - - - +
225B ALA* 1.3 63.2 + - - +
226B VAL* 4.3 2.8 - - + +
402B VAL 3.3 27.4 - - - +
403B THR 3.8 13.0 + - - +
404B HIS* 2.8 29.6 + - - +
405B GLY* 3.6 12.0 - - - +
406B ARG 4.9 0.2 - - - +
407B GLU* 2.2 45.9 + - - +
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Residues in contact with ALA 225 (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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24B LEU* 4.3 9.6 - - + -
25B ARG 3.5 21.1 - - - +
27B GLY* 2.7 30.8 + - - -
28B GLU 2.9 13.2 + - - +
30B LEU* 3.7 12.4 - - + +
211B ASN 3.7 4.7 - - - -
212B CYS* 4.2 0.7 - - - -
224B ARG* 1.3 74.2 - - - +
226B VAL* 1.3 61.6 + - - +
227B ARG 3.6 11.7 - - - +
229B ILE* 3.9 16.2 - - + -
402B VAL* 3.9 0.2 - - - +
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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