Contacts of the strand formed by residues 121 - 126 (chain F) in PDB entry 6Q2J
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 VAL 121 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40F LEU* 5.2 2.5 - - + -
72F LEU* 5.1 16.2 - - + +
73F TYR 3.4 15.9 - - - +
74F GLY* 4.8 0.4 - - - -
80F LEU* 4.0 7.6 - - + -
86F ILE* 5.9 0.7 - - + -
106F TRP* 4.0 22.7 - - + -
109F LEU* 5.0 4.7 - - + -
118F LEU* 3.8 29.4 - - + -
120F THR* 1.3 82.7 - - - +
122F TYR* 1.3 68.6 + - - +
146F TYR* 3.6 1.0 - - - -
147F PHE* 2.9 51.6 + - + +
149F PHE* 5.7 0.6 - - + +
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Residues in contact with TYR 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255D ASP* 6.1 1.1 - - - -
71F HIS 3.9 0.7 - - - +
72F LEU* 3.7 7.3 - - - -
73F TYR* 3.0 58.0 + + + +
74F GLY* 3.3 25.4 - - - -
77F ARG* 3.7 36.3 + - - +
120F THR* 5.1 6.1 - - + -
121F VAL* 1.3 80.7 - - - +
123F LEU* 1.3 76.4 + - - +
124F LYS* 4.9 7.0 - - + -
144F ARG* 4.1 23.9 + - + -
145F VAL 3.2 14.4 - - - +
146F TYR* 3.4 24.7 - + + -
147F PHE* 4.6 3.1 - - - -
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Residues in contact with LEU 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68F LEU* 3.8 19.7 - - + -
69F GLY 4.8 9.9 - - - +
71F HIS 4.2 12.8 - - - +
72F LEU* 3.7 26.2 - - + -
73F TYR* 6.0 0.4 - - - -
83F ASN* 3.8 17.9 - - + +
86F ILE* 3.8 24.9 - - + -
95F LEU* 4.4 3.8 - - + -
122F TYR* 1.3 78.9 - - - +
124F LYS* 1.3 69.7 + - - +
125F VAL* 5.0 0.2 - - + -
144F ARG* 3.1 9.9 - - - +
145F VAL* 2.9 34.6 + - + +
147F PHE* 3.7 25.4 - - + -
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Residues in contact with LYS 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68F LEU* 3.2 2.8 - - - -
69F GLY* 2.5 43.1 + - - +
71F HIS 5.1 2.0 + - - -
73F TYR* 3.6 38.7 + - + +
77F ARG* 3.9 13.2 - - - +
122F TYR* 4.9 5.8 - - + -
123F LEU* 1.3 78.9 - - - +
125F VAL* 1.3 62.0 + - - +
126F PHE* 3.9 25.8 - - + -
135F GLY 2.7 36.2 + - - +
136F GLU* 3.7 1.6 - - - +
137F CYS* 3.7 34.4 - - + +
142F CYS* 4.0 1.3 - - - -
143F ALA 4.1 2.2 - - - -
144F ARG* 4.3 2.0 - - + +
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Residues in contact with VAL 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F PHE* 3.8 11.1 - - + -
53F VAL* 5.3 5.8 - - + -
66F PHE* 4.0 20.6 - - + -
67F ARG 3.5 7.9 - - - +
68F LEU* 3.7 20.2 - - + -
88F ILE* 4.4 7.0 - - + -
95F LEU* 4.6 7.6 - - + -
123F LEU* 5.0 0.9 - - + -
124F LYS* 1.3 78.8 - - - +
126F PHE* 1.3 75.6 + - - +
142F CYS* 3.6 2.4 - - - -
143F ALA* 2.9 41.2 + - + +
145F VAL* 3.7 28.0 - - + -
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Residues in contact with PHE 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F PHE* 4.0 2.4 - - - -
66F PHE* 3.8 3.1 - - - -
67F ARG* 2.9 65.0 + - + +
68F LEU* 5.0 4.7 - - - +
69F GLY* 5.7 3.1 - - - -
124F LYS* 3.9 25.1 - - + -
125F VAL* 1.3 90.9 - - - +
127F LEU* 1.3 64.1 + - - +
128F SER 4.5 13.2 - - - +
129F PRO* 5.7 1.8 - - + -
135F GLY 4.6 18.2 - - - -
136F GLU 6.0 1.1 - - - -
137F CYS* 5.2 0.9 - - + -
141F GLY 4.1 5.8 - - - +
142F CYS* 3.5 32.5 - - + -
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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