Contacts of the strand formed by residues 25 - 32 (chain A) in PDB entry 1TQF
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 GLN 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A MET 3.7 1.2 - - - +
19A THR* 3.6 2.0 - - - +
20A VAL* 2.9 46.9 + - + +
23A PRO* 4.0 7.3 + - + +
24A PRO* 1.3 77.6 - - - +
26A THR* 1.3 62.9 + - - +
27A LEU* 3.9 6.0 + - + +
51A TYR 3.9 4.2 - - - +
52A TYR* 3.5 14.3 - - - -
53A GLN* 2.8 54.9 + - - +
56A LEU* 4.1 14.0 - - + +
57A SER* 4.1 18.2 - - - +
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Residues in contact with THR 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A GLU* 3.9 37.2 - - + +
18A MET 3.3 11.0 - - - +
19A THR* 2.9 26.6 + - - +
24A PRO* 4.0 2.4 + - - +
25A GLN* 1.3 72.3 - - - +
27A LEU* 1.3 72.6 + - - +
50A ARG* 3.2 28.2 + - - +
88A PRO* 5.0 3.2 - - + +
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Residues in contact with LEU 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A GLU* 3.4 3.9 - - - -
18A MET 2.9 32.8 + - - +
20A VAL* 4.6 13.0 - - + -
25A GLN* 4.3 7.4 - - + +
26A THR* 1.3 83.0 - - - +
28A ASN* 1.3 64.0 + - - +
29A ILE* 3.6 13.8 + - + +
40A VAL* 4.0 30.5 - - + -
41A GLY 4.8 1.1 - - - +
50A ARG* 3.7 32.8 - - + +
51A TYR* 4.1 20.0 - - - +
52A TYR* 4.1 20.9 - - + +
116A GLU* 3.7 11.4 - - + +
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Residues in contact with ASN 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ARG* 3.5 20.3 + - - +
15A TYR* 3.6 25.5 - - + -
16A VAL 3.9 2.2 - - - -
17A GLU* 3.5 23.4 - - - +
27A LEU* 1.3 70.1 - - - +
29A ILE* 1.3 58.9 + - - +
50A ARG* 3.2 23.8 + - - +
114A ASN* 3.0 35.7 + - - +
115A TRP* 3.8 2.9 - - - -
116A GLU* 2.8 40.9 + - - +
117A GLY 3.4 4.2 + - - -
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Residues in contact with ILE 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A TYR* 3.0 5.6 - - - +
16A VAL* 2.9 40.9 + - + +
18A MET* 3.7 36.6 - - + -
20A VAL* 6.4 0.4 - - + -
27A LEU* 3.8 15.5 - - + +
28A ASN* 1.3 82.9 - - - +
30A LEU* 1.3 63.9 + - - +
31A VAL 3.4 0.7 + - - -
38A PHE* 4.1 2.5 - - + -
40A VAL* 3.7 29.6 - - + -
117A GLY* 3.7 11.9 - - - +
118A ILE* 3.3 8.3 - - - +
119A LEU* 3.3 39.9 - - + +
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Residues in contact with LEU 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A GLY* 3.6 27.8 - - - -
14A TYR 3.4 19.7 - - - +
15A TYR* 3.8 3.9 - - - +
29A ILE* 1.3 71.0 - - - +
31A VAL* 1.3 67.4 + - - +
32A ASP* 3.4 5.0 + - + -
115A TRP* 3.9 23.7 - - + +
117A GLY 2.9 18.7 + - - +
118A ILE* 3.6 13.8 - - + +
119A LEU* 2.7 31.9 + - - +
229A SER 5.4 0.4 - - - +
230A GLY* 4.9 3.6 - - - -
401A 32P 3.6 50.7 - - + -
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Residues in contact with VAL 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU* 3.9 28.5 - - + -
14A TYR* 2.9 26.9 + - + +
16A VAL* 4.1 18.6 - - + +
29A ILE 4.1 1.3 - - - +
30A LEU* 1.3 75.9 - - - +
32A ASP* 1.3 56.4 + - - +
119A LEU* 4.3 6.3 - - + -
121A LEU* 3.7 23.1 - - + -
152A LEU* 3.8 32.1 - - + -
154A LEU* 5.7 0.9 - - + -
174A MET* 4.3 6.3 - - - -
229A SER* 2.7 30.1 + - - +
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Residues in contact with ASP 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LEU* 3.4 3.8 + - + +
31A VAL* 1.3 76.0 - - - +
33A THR* 1.3 57.2 + - - +
34A GLY* 2.9 9.9 + - - -
35A SER* 2.6 28.7 + - - +
71A TYR* 4.4 0.3 - - - -
118A ILE* 3.3 27.3 - - + +
119A LEU 3.0 15.2 + - - +
120A GLY* 3.3 2.9 - - - -
121A LEU* 2.9 24.5 + - - +
228A ASP* 2.8 26.7 - - - +
229A SER* 3.4 0.7 - - - -
230A GLY* 3.3 13.7 - - - +
401A 32P 4.2 11.6 + - - -
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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