Contacts of the strand formed by residues 105 - 113 (chain F) in PDB entry 4QAE
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 SER 105 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94F LEU* 4.6 7.9 - - - -
104F THR* 1.3 81.5 + - - +
106F GLY* 1.3 61.3 + - - +
125F VAL* 3.3 8.7 - - - +
126F VAL* 3.1 41.8 + - - +
8U ILE* 5.0 2.8 - - - +
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Residues in contact with GLY 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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93F THR* 3.4 26.9 - - - +
94F LEU* 3.4 31.1 + - - +
105F SER* 1.3 81.8 + - - +
107F LEU* 1.3 60.4 + - - +
124F LYS 3.2 11.2 - - - -
125F VAL* 4.2 0.7 - - - -
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Residues in contact with LEU 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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13F LEU* 3.8 39.3 - - + -
91F GLU* 3.8 24.9 - - + +
92F PHE 3.5 11.9 - - - +
93F THR* 4.3 13.0 - - + -
94F LEU* 4.6 0.7 - - - +
106F GLY* 1.3 74.0 - - - +
108F VAL* 1.3 69.0 + - - +
109F ARG* 4.1 15.7 - - + +
122F PHE* 4.5 4.9 - - + -
123F PHE* 3.3 5.5 - - - +
124F LYS* 2.9 49.8 + - + +
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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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56F TYR* 5.0 2.2 - - + +
83F PHE* 3.8 39.5 - - + -
90F GLY 4.5 0.2 - - - -
91F GLU* 3.2 8.0 - - - +
92F PHE* 2.8 51.7 + - + +
94F LEU* 4.2 9.9 - - + -
107F LEU* 1.3 79.8 - - - +
109F ARG* 1.3 64.9 + - - +
110F VAL* 5.0 3.1 - - + +
121F VAL* 3.7 24.5 - - + -
122F PHE* 3.4 4.0 - - - -
123F PHE* 3.8 21.8 - - + -
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Residues in contact with ARG 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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13F LEU* 3.1 45.4 + - - +
16F VAL* 2.8 54.8 + - + -
18F LEU* 3.6 28.4 - - + +
87F SER* 5.0 1.4 + - - -
88F GLN* 3.7 16.2 - - - +
90F GLY 3.6 3.4 - - - -
91F GLU* 2.8 28.0 + - + +
107F LEU* 4.1 14.6 - - + +
108F VAL* 1.3 79.6 - - - +
110F VAL* 1.3 61.1 + - - +
111F VAL* 3.2 6.7 + - + +
121F VAL* 3.4 2.9 - - - -
122F PHE* 2.9 42.3 + - + +
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Residues in contact with VAL 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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17F PRO 4.3 0.4 - - - -
18F LEU* 3.5 7.2 - - - +
19F GLN* 2.8 25.4 + - + +
22F PHE* 3.9 34.8 - - + -
27F PHE* 3.9 37.9 - - + -
56F TYR* 6.1 0.9 - - + -
90F GLY* 2.9 21.1 + - - +
92F PHE* 4.9 6.1 - - + -
108F VAL* 5.1 4.0 - - + -
109F ARG* 1.3 69.1 - - - +
111F VAL* 1.3 60.8 + - - +
112F SER 4.2 5.2 - - - +
113F THR* 4.0 15.0 - - + -
120F MET 4.0 5.8 - - - +
121F VAL* 4.4 9.6 - - + -
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Residues in contact with VAL 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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16F VAL* 3.6 20.9 - - + -
17F PRO* 3.3 37.2 - - + +
18F LEU 3.9 2.4 - - - -
19F GLN* 3.3 17.0 + - - +
109F ARG 3.6 13.2 - - - +
110F VAL* 1.3 74.2 - - - +
112F SER* 1.3 66.1 + - - +
120F MET* 2.8 24.2 + - + +
122F PHE* 4.0 9.9 - - + +
155F PHE* 3.9 28.0 - - + -
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Residues in contact with SER 112 (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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19F GLN* 3.4 10.7 + - - -
110F VAL* 3.5 2.6 - - - +
111F VAL* 1.3 83.8 - - - +
113F THR* 1.3 65.1 + - - +
118F HIS* 4.4 12.6 + - - -
119F ALA* 3.0 4.5 - - - +
120F MET* 2.8 54.8 + - - +
151F ASN* 5.7 1.0 + - - -
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Residues in contact with THR 113 (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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19F GLN* 3.1 24.4 + - + +
22F PHE* 4.8 0.4 - - + -
27F PHE* 3.9 10.8 - - + -
31F TRP* 3.7 4.5 - - - -
110F VAL* 4.0 11.0 - - + -
112F SER* 1.3 79.5 + - - +
114F ASN* 1.3 57.7 + - - +
115F TYR* 2.8 54.8 + - + -
118F HIS* 2.6 26.8 + - - -
119F ALA* 3.6 12.6 - - - +
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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