Contacts of the strand formed by residues 33 - 43 (chain C) in PDB entry 1PL8
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 GLU 33 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29C PRO* 3.7 6.5 - - + +
30C GLY* 2.6 39.0 + - - +
32C ASN* 1.3 84.4 - - - +
34C VAL* 1.3 67.0 + - - +
79C GLY* 2.8 26.2 + - - -
82C VAL* 3.3 3.5 - - - +
133C LYS* 3.4 34.1 - - + +
134C HIS* 3.2 22.1 + - - +
135C ASN* 4.4 5.1 + - + +
136C ALA 4.0 0.4 - - - +
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Residues in contact with VAL 34 (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 PRO* 4.0 5.4 - - - -
33C GLU* 1.3 80.7 - - - +
35C LEU* 1.3 59.7 + - - +
36C LEU* 3.6 25.3 - - + +
75C VAL* 4.4 6.7 - - + -
77C LYS 3.3 8.5 - - - +
78C VAL* 3.8 21.3 - - + -
82C VAL* 3.8 18.6 - - + -
85C LEU* 4.1 10.8 - - + -
133C LYS* 3.2 4.5 - - - -
134C HIS 3.0 32.0 + - - +
136C ALA* 3.9 8.7 - - + -
139C CYS* 3.8 18.8 - - + -
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Residues in contact with LEU 35 (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* 4.2 14.4 - - + -
27C PRO* 3.5 34.5 - - + +
28C GLU* 5.8 0.4 - - - +
29C PRO* 4.0 12.0 - - + +
34C VAL* 1.3 73.2 - - - +
36C LEU* 1.3 56.4 + - - +
75C VAL* 3.6 2.9 - - - +
76C GLU* 2.6 53.7 + - + -
77C LYS* 2.7 33.5 + - + +
131C PHE* 4.1 13.2 - - + -
132C TYR 3.7 26.5 - - - +
133C LYS* 4.2 2.5 - - + +
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Residues in contact with LEU 36 (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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34C VAL* 3.6 29.2 - - + +
35C LEU* 1.3 76.1 - - - +
37C ARG* 1.3 60.8 + - - +
38C MET* 3.3 15.9 + - - +
73C GLY* 5.0 0.7 - - - -
74C THR 3.3 4.7 - - - +
75C VAL* 3.6 30.3 - - + +
76C GLU* 4.6 0.4 - - - -
91C VAL* 3.6 29.2 - - + -
93C ILE* 4.2 10.1 - - + -
131C PHE* 3.2 10.5 - - - -
132C TYR* 2.7 50.0 + - + +
134C HIS* 4.1 10.5 - - + -
139C CYS* 4.1 11.0 - - - -
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Residues in contact with ARG 37 (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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35C LEU 4.2 0.2 + - - -
36C LEU* 1.3 69.8 - - - +
38C MET* 1.3 68.7 + - - +
39C HIS* 4.4 1.0 - - - +
73C GLY* 3.4 0.2 - - - -
74C THR* 2.7 67.0 + - - +
75C VAL 5.1 1.6 + - - -
76C GLU* 3.0 33.6 + - - +
130C ARG* 3.4 7.9 - - + +
131C PHE* 3.9 21.5 - - + -
350C ASP* 2.7 36.3 + - + +
352C SER* 4.5 5.8 + - - -
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Residues in contact with MET 38 (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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36C LEU* 4.2 8.3 - - - +
37C ARG* 1.3 73.9 - - - +
39C HIS* 1.3 58.3 + - - +
41C VAL* 4.0 2.2 - - + -
71C ALA* 3.3 33.9 - - + -
72C SER 3.8 7.4 - - - +
73C GLY* 4.2 0.4 - - - -
93C ILE* 3.6 24.2 - - + -
127C ASN* 3.4 24.0 - - + +
129C CYS 3.1 29.2 - - - +
130C ARG 2.8 15.8 + - - +
132C TYR* 3.7 30.5 - - + -
349C CYS* 3.6 10.5 - - + +
350C ASP* 3.5 22.5 + - - +
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Residues in contact with HIS 39 (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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37C ARG 3.5 1.8 + - - +
38C MET* 1.3 75.5 - - - +
40C SER* 1.3 86.1 + - - +
72C SER 3.1 9.3 + - - +
73C GLY* 3.9 4.7 - - - -
74C THR* 5.0 1.8 - - - +
148C PHE* 3.3 50.2 - + + +
348C LYS* 3.4 12.3 - - - +
349C CYS* 2.8 27.9 + - - -
350C ASP* 3.9 14.4 + - + +
353C ASP* 2.8 46.8 + - + -
355C ASN 3.1 24.7 - - - -
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Residues in contact with SER 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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39C HIS* 1.3 92.2 + - - +
41C VAL* 1.3 64.2 + - - +
71C ALA* 3.1 4.9 - - - +
72C SER* 3.0 37.5 + - - -
148C PHE* 3.6 12.9 - - - +
149C GLU* 3.8 9.7 - - - +
152C ALA* 3.6 7.6 - - - +
346C MET* 4.4 3.6 - - - -
347C LEU 3.4 4.5 - - - -
348C LYS* 2.6 30.7 + - - +
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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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38C MET* 4.0 4.9 - - + -
40C SER* 1.3 78.5 - - - +
42C GLY* 1.3 74.7 + - - +
43C ILE* 3.9 0.5 + - - +
68C GLY* 4.0 6.7 - - - -
69C HIS 4.2 0.2 - - - +
70C GLU 3.2 8.1 - - - +
71C ALA* 3.4 14.8 - - + -
127C ASN* 3.7 35.7 - - - +
128C LEU* 3.8 27.4 - - + -
346C MET* 3.9 2.2 - - - -
347C LEU* 2.8 37.9 + - - +
349C CYS* 3.9 17.7 - - - -
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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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41C VAL* 1.3 83.9 - - - +
43C ILE* 1.3 61.1 + - - +
47C ASP* 4.3 2.3 - - - +
68C GLY* 5.2 0.2 - - - -
69C HIS 4.7 0.9 + - - -
70C GLU* 2.7 41.8 + - - +
344C LYS* 4.1 2.0 - - - -
345C ILE 3.4 10.5 - - - -
346C MET* 3.7 20.7 - - - +
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Residues in contact with ILE 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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41C VAL 4.5 1.1 - - - +
42C GLY* 1.3 77.2 - - - +
44C CYS* 1.3 62.5 + - - +
47C ASP* 3.5 15.9 - - + +
48C VAL* 4.9 2.2 - - + -
70C GLU* 4.3 0.4 - - - -
128C LEU* 4.0 15.0 - - + -
333C ALA* 4.2 13.2 - - + +
334C PHE* 3.9 30.1 - - + -
337C PHE* 4.3 21.3 - - + -
343C LEU 5.4 0.2 - - - +
344C LYS* 2.9 21.1 + - - +
345C ILE* 3.2 37.3 + - + +
347C LEU* 3.6 27.1 - - + -
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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