Contacts of the strand formed by residues 105 - 111 (chain F) in PDB entry 3QAZ
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 THR 105 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69F TYR* 3.1 28.1 - - - -
70F LYS* 3.2 31.6 + - + -
71F ASN* 6.2 0.4 - - - +
72F SER* 5.7 0.4 - - - -
104F GLN* 1.3 71.6 - - - +
106F PHE* 1.3 67.1 + - - +
107F VAL* 4.9 2.2 - - + -
123F MET* 4.8 16.8 - - + -
124F LEU 4.0 9.6 - - - +
125F LYS* 5.7 6.4 - - + +
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Residues in contact with PHE 106 (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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48F MET* 3.4 32.3 - - + -
50F CYS* 4.3 4.5 - - - -
65F LEU* 6.2 0.2 - - + -
67F TYR* 3.9 19.1 - + + -
68F TRP 4.8 0.9 - - - -
69F TYR* 3.3 32.3 - + + -
95F LEU* 3.7 20.9 - - + -
104F GLN 3.2 1.9 + - - +
105F THR* 1.3 72.8 - - - +
107F VAL* 1.3 62.5 + - - +
108F VAL* 3.1 30.5 - - + -
122F GLN 4.0 0.3 - - - +
123F MET* 3.7 2.4 - - - -
124F LEU* 2.8 59.1 + - + +
126F LEU* 3.3 34.1 - - + -
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Residues in contact with VAL 107 (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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67F TYR* 3.0 10.3 - - - +
68F TRP* 2.8 85.1 + - + +
70F LYS* 4.5 20.6 - - + +
105F THR* 4.7 2.9 - - + +
106F PHE* 1.3 78.8 - - - +
108F VAL* 1.3 73.7 + - - +
121F THR* 4.5 9.2 - - - -
122F GLN 3.6 11.4 - - - +
123F MET* 4.4 18.6 - - + -
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Residues in contact with VAL 108 (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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38F VAL* 4.7 12.3 - - + +
40F CYS* 4.3 10.8 - - - -
50F CYS* 4.8 2.7 - - + -
65F LEU* 4.8 13.0 - - + -
66F HIS 3.6 3.8 - - - +
67F TYR* 4.4 3.8 - - + -
106F PHE* 3.1 42.6 - - + -
107F VAL* 1.3 75.3 - - - +
109F GLN* 1.3 61.2 + - - +
110F LEU 4.2 0.4 - - - -
120F ALA 3.6 1.4 - - - +
121F THR* 3.3 23.7 - - - -
122F GLN* 3.4 33.0 + - - +
124F LEU* 4.2 13.2 - - + -
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Residues in contact with GLN 109 (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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64F THR 3.4 2.1 - - - +
65F LEU* 3.3 8.8 - - - +
66F HIS* 2.6 58.5 + - + +
68F TRP* 2.7 39.5 - - + -
77F VAL* 5.3 0.9 - - - +
108F VAL* 1.3 76.5 - - - +
110F LEU* 1.3 59.9 + - - +
111F GLN* 3.8 2.2 + - + -
119F GLN* 3.0 31.0 + - + +
120F ALA 3.5 1.8 - - - +
121F THR* 3.4 21.2 - - + +
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Residues in contact with LEU 110 (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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35F LEU* 3.5 40.3 - - + +
36F PRO* 3.3 14.8 - - + +
38F VAL* 3.3 35.0 - - + -
52F TRP* 3.9 31.2 - - + -
63F LEU* 3.8 25.8 - - + -
64F THR 3.6 3.1 - - - +
65F LEU* 4.8 2.9 - - + +
108F VAL 4.2 0.6 - - - -
109F GLN* 1.3 73.8 - - - +
111F GLN* 1.3 60.4 + - - +
119F GLN* 3.5 5.1 - - - +
120F ALA* 3.0 33.2 + - + +
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Residues in contact with GLN 111 (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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63F LEU* 3.1 15.5 - - - +
64F THR* 2.7 54.9 + - - +
66F HIS* 4.6 10.5 - - + +
109F GLN* 4.8 2.5 - - + +
110F LEU* 1.3 77.5 - - - +
112F ASP* 1.3 75.8 + - - +
113F PRO* 3.7 11.1 - - + +
115F GLU 4.3 0.2 - - - +
116F PRO* 4.1 22.7 + - - +
118F ARG 2.9 26.2 - - - +
119F GLN* 4.0 9.9 - - + +
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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