Contacts of the strand formed by residues 15 - 22 (chain C) in PDB entry 3QTE
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 15 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A ARG* 4.8 10.5 - - - -
23A MET* 3.8 36.1 - - + +
25A ILE* 3.3 31.6 - - + -
27A TRP* 3.4 25.7 - + - -
10C CYS* 4.3 3.4 - - - -
13C THR 4.4 10.3 - - - -
14C GLU* 1.3 80.6 - - - +
16C SER* 1.3 62.6 + - - +
17C TYR* 3.2 7.6 + - - +
30C CYS* 3.4 2.3 - - - -
31C CYS* 2.8 39.9 + - - +
32C LEU* 4.8 4.5 - - - -
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Residues in contact with SER 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A MET 4.5 5.1 - - - +
25A ILE* 6.2 0.2 - - - +
10C CYS* 3.8 17.5 - - - +
14C GLU 4.4 0.2 + - - -
15C TYR* 1.3 70.9 - - - +
17C TYR* 1.3 62.8 + - - +
18C GLY 4.4 4.2 + - - -
28C ARG* 2.9 44.9 + - - +
29C PHE 4.0 0.7 - - - -
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Residues in contact with TYR 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A MET* 3.2 37.9 - - + -
24A GLY* 3.5 21.2 - - - -
17B TYR* 2.8 61.9 + + - -
18B GLY* 3.5 12.3 - - - -
19B THR 3.6 12.7 + - - -
29B PHE* 3.7 21.1 - + - -
15C TYR 3.2 2.8 + - - +
16C SER* 1.3 76.0 - - - +
18C GLY* 1.3 55.6 + - - +
29C PHE* 2.9 23.4 + + - +
31C CYS* 4.2 12.1 - - - -
33C GOL 4.1 10.6 + - - -
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Residues in contact with GLY 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B TYR* 3.3 14.7 + - - -
16C SER* 4.4 4.7 + - - -
17C TYR* 1.3 78.1 - - - +
19C THR* 1.3 62.3 + - - +
28C ARG* 3.5 7.1 - - - +
29C PHE* 2.7 34.8 + - - +
33C GOL 3.3 15.7 - - - -
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Residues in contact with THR 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B TYR* 3.7 9.3 + - - -
18C GLY* 1.3 78.4 - - - +
20C CYS* 1.3 64.3 + - - +
21C THR* 3.8 11.6 + - - -
26C ASN* 4.1 18.6 + - + +
27C TRP 3.1 13.7 - - - +
28C ARG* 5.3 2.7 - - + -
29C PHE* 4.1 2.5 - - - +
33C GOL 3.5 22.9 + - - +
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Residues in contact with CYS 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C CYS* 2.0 59.5 - - + -
19C THR* 1.3 72.4 - - - +
21C THR* 1.3 61.1 + - - +
22C VAL* 5.3 3.4 - - + -
26C ASN* 4.5 0.4 - - - -
27C TRP* 2.9 41.2 + - + -
28C ARG 4.0 6.5 - - - -
29C PHE* 3.6 20.2 - - - -
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Residues in contact with THR 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C THR* 3.8 10.7 + - - -
20C CYS* 1.3 73.0 - - - +
22C VAL* 1.3 67.1 + - - +
23C MET 4.1 0.9 + - - -
24C GLY* 3.8 26.7 - - - +
25C ILE 3.5 2.7 - - - +
26C ASN* 2.5 28.2 + - - +
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Residues in contact with VAL 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C CYS* 4.9 4.5 - - + +
21C THR* 1.3 77.9 - - - +
23C MET* 1.3 82.6 + - + +
24C GLY 3.2 0.2 - - - -
25C ILE* 2.8 36.5 + - - +
27C TRP* 3.1 33.7 - - + -
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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