Contacts of the strand formed by residues 97 - 102 (chain G) in PDB entry 1QZW
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 PHE 97 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91G ASN 5.3 1.1 - - - -
92G PRO* 4.2 6.3 - - + -
93G THR* 3.1 42.0 - - - -
94G LYS* 3.0 33.2 - - + -
95G LEU* 5.3 0.2 - - + -
96G PRO* 1.3 96.7 - - - +
98G ILE* 1.3 68.4 + - - +
99G ILE* 4.0 8.5 - - + -
180G ASP 3.1 8.8 + - - +
181G ILE* 4.3 19.7 - - + -
182G ILE* 3.5 28.1 + - - +
212G ASP* 3.5 34.8 - - + -
213G ASP* 3.8 27.1 - - + -
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Residues in contact with ILE 98 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97G PHE* 1.3 78.9 - - - +
99G ILE* 1.3 56.6 + - - +
100G MET* 3.3 3.0 + - - +
171G VAL* 6.0 7.0 - - + -
182G ILE* 4.5 3.6 - - + -
184G VAL* 6.3 1.3 - - + -
209G LEU* 3.3 29.4 - - + -
210G LYS 2.8 30.5 - - - +
211G PRO* 3.1 26.9 - - + +
212G ASP* 3.2 24.7 + - - +
213G ASP 2.6 33.1 + - - +
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Residues in contact with ILE 99 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97G PHE* 4.3 11.9 - - + -
98G ILE* 1.3 74.3 - - - +
100G MET* 1.3 57.8 + - - +
101G LEU* 3.2 17.7 + - + -
116G LEU* 4.6 10.1 - - + -
181G ILE* 5.3 5.6 - - + -
182G ILE* 2.8 25.0 + - - +
183G ILE* 3.3 35.4 - - + -
184G VAL* 3.0 24.3 + - - +
213G ASP* 3.4 32.1 - - + -
215G ILE* 4.3 11.4 - - + -
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Residues in contact with MET 100 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98G ILE* 3.3 2.9 + - - -
99G ILE* 1.3 71.0 - - - +
101G LEU* 1.3 63.0 + - - +
102G VAL* 3.8 15.3 - - + -
184G VAL* 4.2 2.7 - - - -
186G THR* 4.8 5.8 - - + -
202G MET* 4.0 13.5 - - - -
205G MET* 2.9 42.6 - - + +
206G TYR* 3.2 30.5 - - - +
209G LEU* 3.6 22.4 - - + -
211G PRO* 3.9 10.8 - - + -
213G ASP 3.0 7.7 + - - -
214G VAL* 3.4 20.5 - - + +
215G ILE* 2.9 29.3 + - - +
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Residues in contact with LEU 101 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99G ILE* 3.2 17.4 + - + +
100G MET* 1.3 79.2 - - - +
102G VAL* 1.3 66.3 + - - +
109G LYS 4.6 5.2 - - - +
112G THR* 5.3 4.5 - - - +
113G ALA* 6.1 2.5 - - + +
116G LEU* 5.4 7.2 - - + -
183G ILE* 5.3 4.0 - - + -
184G VAL 2.9 24.8 + - - +
185G ASP* 3.2 24.6 - - + +
186G THR* 2.4 38.0 + - - +
215G ILE* 3.4 34.1 - - + +
217G VAL* 4.2 22.4 - - + -
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Residues in contact with VAL 102 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100G MET* 3.5 18.1 + - + -
101G LEU* 1.3 75.3 - - - +
103G GLY* 1.3 58.8 + - - +
186G THR* 3.6 11.0 - - + -
187G ALA* 5.7 0.2 - - - +
198G LEU* 6.0 3.8 - - + -
202G MET* 3.2 42.4 - - + -
205G MET* 5.4 0.2 - - - -
214G VAL* 4.1 9.2 - - + -
215G ILE 2.8 26.2 + - - +
216G LEU* 2.9 33.6 - - + +
217G VAL 3.7 1.2 + - - -
233G PHE* 5.2 6.1 - - + -
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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