Contacts of the strand formed by residues 98 - 105 (chain Q) in PDB entry 5FYW
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 TYR 98 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97Q GLU* 1.3 104.3 + - - +
99Q ASN* 1.3 79.0 + - - +
100Q GLU* 4.1 15.3 - - + -
96R ARG* 3.1 49.9 + - + -
97R ILE 2.8 14.1 - - - +
98R ASN* 4.2 10.8 - - + -
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Residues in contact with ASN 99 (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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97Q GLU* 4.8 4.4 - - - +
98Q TYR* 1.3 94.2 + - - +
100Q GLU* 1.3 59.4 + - - +
101Q PHE* 3.4 30.6 - - + -
95R ILE 3.3 3.1 - - - +
96R ARG* 2.9 2.0 - - - -
97R ILE* 2.4 48.4 + - + +
99R LYS* 2.8 34.2 + - - +
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Residues in contact with GLU 100 (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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98Q TYR* 4.1 12.7 + - + -
99Q ASN* 1.3 71.1 - - - +
101Q PHE* 1.3 65.9 + - - +
102Q PRO* 4.0 5.7 - - - +
94R LYS* 5.5 10.7 - - + +
95R ILE 3.0 7.0 - - - +
96R ARG* 2.5 59.8 + - + -
107R LEU* 5.1 11.8 - - + +
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Residues in contact with PHE 101 (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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99Q ASN* 3.4 34.8 - - + -
100Q GLU* 1.3 73.0 - - - +
102Q PRO* 1.3 65.3 - - + +
103Q LEU* 4.6 0.2 - - - +
381Q ASP* 4.4 6.7 - - - -
382Q GLY* 3.1 49.8 - - - +
383Q SER* 3.8 1.8 - - - -
384Q PHE* 4.3 6.9 - + + -
94R LYS* 4.1 1.1 - - - -
95R ILE* 2.2 56.7 + - - +
97R ILE* 3.4 26.2 - - + -
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Residues in contact with PRO 102 (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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100Q GLU 4.0 5.6 - - - +
101Q PHE* 1.3 91.2 - - + +
103Q LEU* 1.3 65.0 + - - +
104Q ARG* 5.5 12.1 - - + +
383Q SER* 3.3 23.1 - - - +
384Q PHE* 2.9 25.5 + - - -
92R LEU* 5.4 3.6 - - + -
93R GLY 3.5 5.6 - - - +
94R LYS* 3.5 23.8 - - + -
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Residues in contact with LEU 103 (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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102Q PRO* 1.3 75.5 - - - +
104Q ARG* 1.3 68.4 + - - +
376Q LEU* 3.8 3.6 - - + -
384Q PHE* 3.5 33.9 - - + -
386Q MET* 3.6 35.4 - - + -
81R TRP* 5.8 1.6 - - + -
92R LEU* 3.1 20.5 - - - +
93R GLY* 2.5 31.7 + - - +
95R ILE* 3.5 40.8 - - + -
106R LEU* 3.6 23.6 - - + -
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Residues in contact with ARG 104 (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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102Q PRO* 5.5 11.3 - - + +
103Q LEU* 1.3 83.9 - - - +
105Q ALA* 1.3 66.9 + - - +
106Q ILE 3.8 0.2 + - - -
383Q SER* 6.6 0.4 - - - -
384Q PHE 3.2 11.6 + - - +
385Q THR* 3.6 11.3 - - + -
386Q MET* 3.3 29.5 + - - +
92R LEU* 3.5 28.9 - - + +
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Residues in contact with ALA 105 (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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104Q ARG* 1.3 76.6 - - - +
106Q ILE* 1.3 67.4 + - - +
107Q PRO* 3.7 3.5 - - - +
386Q MET* 4.6 8.1 - - - +
92R LEU* 4.7 7.9 - - + +
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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