Contacts of the strand formed by residues 39 - 49 (chain C) in PDB entry 1Z9N
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 39 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30C GLN* 3.1 5.6 - - - +
31C GLN* 2.7 61.8 + - + +
33C ASP* 6.3 0.2 - - + -
37C GLY 4.2 7.2 - - - +
38C ASN* 1.3 79.9 - - - +
40C ASP* 1.3 66.7 + - - +
41C VAL* 3.8 3.2 - - + +
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Residues in contact with ASP 40 (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 VAL 4.0 5.3 - - - +
30C GLN* 2.8 32.6 + - - +
39C LYS* 1.3 73.1 - - - +
41C VAL* 1.3 62.2 + - - +
42C GLY 3.7 2.9 - - - +
60C HIS* 3.6 15.9 - - - +
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Residues in contact with VAL 41 (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 VAL* 3.1 36.5 + - + +
31C GLN* 3.8 26.7 - - + +
39C LYS* 3.8 11.7 - - + +
40C ASP* 1.3 78.4 - - - +
42C GLY* 1.3 58.1 + - - +
59C LEU* 3.1 11.6 - - + +
60C HIS* 2.9 56.0 + - - +
61C ASP* 4.4 8.5 - - + +
62C LEU* 3.9 19.7 - - + -
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Residues in contact with GLY 42 (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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28C PRO* 3.8 1.0 - - - +
29C VAL 3.0 24.1 + - - +
40C ASP* 3.7 3.2 - - - +
41C VAL* 1.3 80.1 - - - +
43C THR* 1.3 68.9 + - - +
58C LYS 3.5 7.9 - - - -
59C LEU* 3.8 3.6 - - - -
60C HIS* 3.8 9.8 + - - -
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Residues in contact with THR 43 (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 VAL* 3.7 29.6 - - + +
27C VAL 3.1 12.8 - - - +
28C PRO* 4.2 7.9 - - + -
29C VAL* 4.4 0.7 - - - -
42C GLY* 1.3 80.0 - - - +
44C VAL* 1.3 61.5 + - - +
45C GLU* 4.7 3.5 + - - +
58C LYS* 2.8 55.6 + - - +
59C LEU* 3.4 7.5 - - - +
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Residues in contact with VAL 44 (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* 2.8 39.8 + - + +
29C VAL* 4.1 11.4 - - + -
43C THR* 1.3 79.9 - - - +
45C GLU* 1.3 71.2 + - - +
46C ILE* 4.7 1.3 - - + -
55C PHE* 4.1 16.6 - - + -
56C THR 3.6 18.4 - - - +
57C PRO* 4.1 7.9 - - + -
59C LEU* 4.0 22.0 - - + -
69C PHE* 4.4 11.0 - - + -
148C LEU* 3.9 28.3 - - + -
150C ILE* 5.3 0.7 - - + -
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Residues in contact with GLU 45 (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 LYS* 3.2 38.5 + - + +
25C ILE 3.3 4.7 - - - +
26C VAL* 4.4 15.6 - - + +
43C THR* 4.7 6.3 + - - +
44C VAL* 1.3 75.3 - - - +
46C ILE* 1.3 62.6 + - - +
47C THR* 4.1 6.7 + - + +
54C VAL 3.4 2.9 - - - +
55C PHE* 3.6 1.4 - - - -
56C THR* 2.8 48.4 + - - +
58C LYS* 2.9 43.9 + - + +
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Residues in contact with ILE 46 (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 LYS* 3.3 8.7 - - - +
25C ILE* 2.8 44.4 + - + +
27C VAL* 3.8 24.9 - - + -
44C VAL* 4.6 2.0 - - + +
45C GLU* 1.3 76.3 - - - +
47C THR* 1.3 63.0 + - - +
53C LEU* 4.1 22.9 - - + -
54C VAL 3.3 8.3 - - - +
55C PHE* 3.7 35.9 - - + -
140C LEU* 3.6 17.9 - - + +
143C VAL* 4.2 7.9 - - + -
148C LEU* 5.1 1.3 - - + -
176C ILE* 4.0 22.9 - - + -
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Residues in contact with THR 47 (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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23C GLU 4.1 8.1 - - - +
24C LYS* 3.8 19.7 - - + -
45C GLU* 5.1 7.0 - - + +
46C ILE* 1.3 80.4 - - - +
48C GLU* 1.3 67.2 + - - +
53C LEU* 3.3 6.6 - - - +
54C VAL* 2.8 49.6 + - - +
56C THR* 4.9 3.5 + - - +
140C LEU* 4.1 6.3 - - - -
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Residues in contact with GLU 48 (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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23C GLU* 4.8 7.6 + - - +
47C THR* 1.3 79.4 + - - +
49C SER* 1.3 63.3 + - - +
53C LEU* 3.6 23.1 - - + -
54C VAL* 5.2 0.4 - - - -
138C LYS 3.7 6.3 - - - +
139C LYS* 3.2 35.4 + - - +
140C LEU* 3.0 37.8 + - + +
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Residues in contact with SER 49 (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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48C GLU* 1.3 78.5 - - - +
50C ALA* 1.3 59.7 + - - +
51C TYR* 3.0 19.3 + - - -
52C GLY* 2.7 34.6 + - - +
54C VAL* 3.9 15.7 - - - -
133C LEU* 3.8 6.6 - - - +
138C LYS 5.3 2.4 - - - +
108D TRP* 3.8 22.2 - - - +
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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