Contacts of the strand formed by residues 220 - 225 (chain A) in PDB entry 5HI7
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A ARG* 3.0 44.0 + - + +
33A SER* 3.6 28.3 + - - -
34A ASP* 2.9 28.1 + - - +
216A PHE* 3.3 4.3 - - - -
217A ASN* 2.8 49.1 + - + +
219A PRO* 1.3 78.7 - - + +
221A LEU* 1.3 59.6 + - - +
222A LEU* 3.7 19.6 + - + +
407A GLU 6.1 0.2 - - - -
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Residues in contact with LEU 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A PHE 4.8 0.7 - - - +
32A ARG* 3.3 9.2 - - - +
33A SER 3.0 35.8 + - - +
183A PHE* 4.5 6.3 - - + -
198A TYR* 3.7 30.3 - - + -
201A ILE* 3.7 43.3 - - + -
214A ILE* 4.3 10.5 - - + -
215A VAL 3.6 5.8 - - - +
216A PHE* 3.7 30.5 - - + -
219A PRO 3.5 0.6 + - - -
220A HIS* 1.3 73.4 - - - +
222A LEU* 1.3 80.0 + - - +
223A LEU* 3.8 5.4 - - + +
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Residues in contact with LEU 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A LEU* 4.1 14.4 - - + -
31A PHE 3.7 1.6 - - - -
32A ARG* 3.7 31.2 - - + +
213A SER 3.7 1.0 - - - +
214A ILE* 3.3 5.0 - - - -
215A VAL* 2.8 42.4 + - + +
217A ASN* 5.3 2.9 - - + -
220A HIS* 3.7 18.6 - - + +
221A LEU* 1.3 83.8 - - - +
223A LEU* 1.3 60.6 + - - +
224A ARG* 4.0 12.8 + - + +
404A HIS 3.8 20.2 - - - +
407A GLU* 4.2 5.6 - - + +
408A HIS* 4.0 35.9 - - + +
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Residues in contact with LEU 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A VAL* 5.5 0.2 - - + -
18A LEU* 4.4 13.5 - - + -
29A LEU* 3.5 5.7 - - - +
30A LEU* 2.9 49.0 + - + -
31A PHE* 2.8 33.3 + - + +
201A ILE* 4.5 5.4 - - + -
204A LEU* 3.5 41.3 - - + -
212A CYS* 3.8 18.6 - - + -
213A SER 3.7 13.0 - - - +
214A ILE* 3.8 9.4 - - + -
221A LEU* 3.8 11.3 - - + +
222A LEU* 1.3 70.9 - - - +
224A ARG* 1.3 63.6 + - - +
237A ILE* 4.1 0.9 - - + -
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Residues in contact with ARG 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A GLY 2.9 28.4 + - - +
28A GLU 3.3 9.2 - - - +
29A LEU* 3.6 30.3 - - + +
30A LEU* 4.3 2.9 - - - -
212A CYS* 3.2 7.0 - - - +
213A SER* 2.9 37.8 + - - +
222A LEU* 4.2 15.2 - - + +
223A LEU* 1.3 81.9 - - - +
225A ALA* 1.3 63.7 + - - +
226A VAL* 5.5 0.2 - - + -
401A ARG 5.0 1.0 + - - -
402A VAL 3.3 18.7 + - - +
403A THR 3.2 26.5 - - - +
404A HIS 2.8 28.4 + - - -
405A GLY* 3.8 9.6 - - - -
406A ARG* 4.7 1.4 - - - +
407A GLU* 3.0 28.9 + - - -
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Residues in contact with ALA 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LEU* 4.3 11.0 - - + -
25A ARG 3.6 18.4 - - - +
27A GLY* 2.6 33.8 + - - -
28A GLU 3.1 9.8 + - - +
30A LEU* 4.0 9.5 - - + +
211A ASN 3.6 5.8 - - - -
212A CYS* 4.2 2.7 - - - -
224A ARG* 1.3 71.9 - - - +
226A VAL* 1.3 58.8 + - - +
227A ARG 3.4 5.8 - - - +
229A ILE* 3.8 24.2 - - + -
402A VAL* 3.8 1.6 - - - +
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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