Contacts of the strand formed by residues 25 - 33 (chain C) in PDB entry 3QEL
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 LYS 25 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24C PRO* 1.3 72.3 - - - +
26C ILE* 1.3 61.8 + - - +
27C VAL* 3.9 4.2 + - + +
57C LYS 2.8 13.2 + - - +
58C ILE* 3.5 9.1 - - + +
59C GLN* 2.8 28.2 + - - +
317C PHE* 5.6 9.2 - - + -
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Residues in contact with ILE 26 (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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24C PRO* 3.6 11.9 + - + +
25C LYS* 1.3 76.6 - - - +
27C VAL* 1.3 62.7 + - - +
28C ASN* 3.6 13.2 - - - +
59C GLN* 3.4 22.7 - - + +
61C GLN* 3.1 42.0 - - + +
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Residues in contact with VAL 27 (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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25C LYS* 5.6 2.9 - - + -
26C ILE* 1.3 75.5 - - - +
28C ASN* 1.3 62.5 + - - +
29C ILE* 4.0 0.8 + - + -
58C ILE* 3.8 22.9 - - + -
59C GLN 3.2 4.3 + - - +
60C LEU* 3.3 35.6 - - + +
61C GLN 2.9 23.4 + - - -
88C TYR* 3.4 43.3 - - + +
313C ILE* 4.4 4.7 - - + -
317C PHE* 3.6 20.6 - - + -
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Residues in contact with ASN 28 (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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26C ILE* 3.6 13.9 - - - +
27C VAL* 1.3 75.6 - - - +
29C ILE* 1.3 62.8 + - - +
61C GLN* 3.2 49.2 + - - +
63C THR* 4.1 9.3 + - - +
85C SER* 3.0 28.8 + - - +
86C GLN* 3.5 13.3 + - - +
87C VAL* 3.1 10.5 - - + -
88C TYR* 2.9 29.7 + - - +
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Residues in contact with ILE 29 (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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27C VAL* 6.2 0.2 - - + -
28C ASN* 1.3 78.3 - - - +
30C GLY* 1.3 70.5 + - - +
42C PHE* 3.6 15.8 - - + -
46C VAL* 4.6 13.9 - - + -
60C LEU* 4.1 35.0 - - + -
61C GLN 2.9 9.1 + - - +
62C ALA 3.6 0.3 - - - -
63C THR* 3.0 26.9 + - - +
87C VAL* 3.7 1.8 - - - -
88C TYR* 4.9 1.3 - - + +
89C ALA 4.1 9.4 - - - +
91C LEU* 3.9 20.4 - - + -
306C VAL* 5.0 7.4 - - + +
309C VAL* 3.5 30.1 - - + -
310C ALA* 4.8 2.2 - - - +
313C ILE* 5.1 5.2 - - + -
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Residues in contact with GLY 30 (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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29C ILE* 1.3 80.7 - - - +
31C ALA* 1.3 61.3 - - - +
42C PHE* 4.2 0.2 - - - -
63C THR 3.1 7.6 - - - -
82C LEU* 4.0 7.6 - - - -
87C VAL* 3.3 16.7 - - - +
89C ALA 2.8 16.4 + - - +
90C ILE* 3.1 11.5 - - - -
91C LEU* 2.9 20.3 + - - +
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Residues in contact with ALA 31 (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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30C GLY* 1.3 75.6 - - - +
32C VAL* 1.3 69.9 + - - +
33C LEU* 3.9 16.4 - - + -
42C PHE* 3.4 36.1 - - + -
63C THR 2.8 6.7 + - - -
64C SER* 3.4 4.0 - - - -
65C VAL 3.1 22.2 + - - -
82C LEU* 3.7 5.6 - - - +
90C ILE* 4.4 0.4 - - - -
91C LEU* 3.3 15.9 - - + +
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Residues in contact with VAL 32 (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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31C ALA* 1.3 81.1 - - - +
33C LEU* 1.3 59.7 + - - +
65C VAL* 3.4 11.7 - - + -
66C THR 4.4 2.2 - - - -
67C HIS* 3.7 29.6 - - + +
74C MET* 4.0 25.6 - - + -
82C LEU* 3.7 22.2 - - + -
90C ILE* 4.2 9.2 - - + -
91C LEU 2.8 10.9 + - - +
92C VAL* 4.2 8.7 - - + -
93C SER* 3.0 26.9 + - - -
107C ILE* 4.3 13.5 - - + -
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Residues in contact with LEU 33 (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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31C ALA* 3.9 17.3 - - + -
32C VAL* 1.3 82.7 - - - +
34C SER* 1.3 63.1 + - - +
35C THR 3.7 1.6 - - - +
38C HIS* 3.4 32.5 - - + +
39C GLU* 3.6 14.6 - - + +
42C PHE* 3.4 27.4 - - + -
64C SER* 4.9 0.4 - - - -
65C VAL 3.0 10.7 + - - +
66C THR* 3.2 23.6 - - - -
67C HIS* 3.3 10.8 + - - -
91C LEU* 4.7 3.1 - - + +
93C SER* 3.2 9.0 - - - +
121C LEU* 4.1 24.2 - - + -
298C GLU* 3.7 13.2 - - - +
302C ILE* 4.1 7.0 - - + -
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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