Contacts of the strand formed by residues 89 - 94 (chain Q) in PDB entry 1HI0
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 89 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45Q SER 5.4 0.3 - - - +
51Q LEU* 5.1 0.9 - - - +
54Q LYS* 3.6 13.2 + - - -
86Q GLY 2.7 28.7 - - - +
87Q MET 2.7 9.9 + - - +
88Q ARG* 1.3 75.6 - - - +
90Q MET* 1.3 68.3 + - - +
91Q ASN* 3.1 17.1 + - - +
206Q GLN 5.8 0.2 - - - -
207Q SER 3.5 22.2 - - - +
208Q THR* 3.9 0.2 - - - -
209Q ASP* 3.2 38.0 + - + -
210Q ALA 5.2 0.2 - - - -
211Q ILE* 3.5 22.5 - - + +
222Q SER* 5.4 0.2 - - - -
247Q LYS* 5.0 7.9 - - + -
264Q PHE* 4.4 1.2 - - - -
265Q PHE* 3.2 15.0 + - + +
266Q CYS 3.4 22.9 + - - -
267Q GLU* 4.3 12.5 - - + -
268Q ARG 5.4 1.1 - - - -
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Residues in contact with MET 90 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45Q SER* 4.6 1.8 - - - -
46Q VAL* 4.0 18.2 - - + -
51Q LEU* 3.2 44.6 - - + -
89Q HIS* 1.3 72.0 - - - +
91Q ASN* 1.3 65.8 + - - +
92Q GLY 3.1 0.2 + - - -
93Q PHE* 3.0 29.3 + - + +
249Q ALA* 4.1 12.3 - - + -
252Q LEU* 3.8 30.5 - - + -
258Q ILE* 5.2 1.1 - - - -
259Q ASP 5.1 0.9 - - - +
260Q VAL* 4.6 13.9 - - - -
264Q PHE* 3.4 29.8 - - + -
265Q PHE 2.8 19.3 + - - +
266Q CYS* 5.1 0.2 - - - -
267Q GLU* 4.4 1.1 - - - +
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Residues in contact with ASN 91 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36Q ALA* 3.7 2.9 - - - -
37Q ILE* 3.4 31.0 + - + +
39Q THR* 4.6 1.8 + - - -
45Q SER* 2.8 37.9 + - - -
54Q LYS* 3.1 25.4 - - - +
89Q HIS* 3.1 9.8 + - - +
90Q MET* 1.3 68.8 - - - +
92Q GLY* 1.3 57.7 + - - +
93Q PHE* 4.3 0.5 - - - -
207Q SER 3.8 10.0 - - - +
267Q GLU* 3.2 21.8 - - - +
526Q PHE 3.5 11.7 + - - -
527Q SER* 3.6 22.0 + - - +
528Q PRO* 4.5 3.4 - - - +
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Residues in contact with GLY 92 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34Q GLU* 3.6 3.5 - - - +
35Q GLY 3.0 38.5 + - - +
37Q ILE* 3.5 12.7 - - - +
91Q ASN* 1.3 73.9 - - - +
93Q PHE* 1.3 59.8 + - - +
94Q PRO* 3.6 8.3 - - - +
267Q GLU* 2.9 14.9 + - - -
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Residues in contact with PHE 93 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34Q GLU* 3.4 19.1 - - + +
35Q GLY* 3.5 14.8 - - - -
36Q ALA* 3.3 33.7 - - + -
46Q VAL* 3.8 17.0 - - + -
90Q MET* 3.0 20.6 + - + +
91Q ASN 4.3 0.4 - - - -
92Q GLY* 1.3 78.8 - - - +
94Q PRO* 1.3 57.0 - - - +
252Q LEU* 3.2 42.6 - - + -
256Q TYR* 3.6 18.8 - + - -
258Q ILE* 3.7 19.7 - - + -
266Q CYS* 3.3 15.6 - - - +
267Q GLU* 2.7 33.6 + - - +
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Residues in contact with PRO 94 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32Q PHE* 3.5 26.7 - - + -
33Q LYS 4.8 0.4 - - - +
34Q GLU* 3.4 17.9 - - + +
92Q GLY 3.6 9.2 - - - +
93Q PHE* 1.3 86.3 - - - +
95Q MET* 1.3 69.4 + - - +
96Q ILE* 3.8 0.3 + - - +
251Q ARG* 3.1 22.0 + - - -
266Q CYS* 3.4 5.7 - - - +
267Q GLU* 3.4 10.7 - - + +
269Q ARG* 3.5 46.2 - - + +
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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