Contacts of the strand formed by residues 38 - 51 (chain C) in PDB entry 2P80
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 VAL 38 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C ILE* 4.3 9.9 - - + +
12C LEU* 4.8 3.9 - - + +
13C PRO 3.2 6.9 + - - -
14C ARG* 3.1 64.4 - - + +
15C GLN 3.2 12.3 + - - -
37C LYS* 1.3 69.1 - - - +
39C VAL* 1.3 60.6 + - - +
40C GLU* 3.6 3.8 + - + +
80C TYR* 3.3 26.7 - - + +
82C GLU* 3.9 33.7 - - + +
123C ARG* 4.3 8.1 - - - -
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Residues in contact with VAL 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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15C GLN* 3.5 21.5 - - + +
17C VAL* 4.2 6.3 - - + -
37C LYS* 3.5 12.6 - - + +
38C VAL* 1.3 73.2 - - - +
40C GLU* 1.3 59.8 + - - +
41C PHE* 3.3 30.9 + - + -
74C VAL 5.0 2.7 - - - +
75C VAL* 3.5 33.9 - - + -
79C ASP* 4.1 4.7 - - + +
80C TYR 2.9 17.6 + - - +
81C LEU* 3.8 1.7 - - - -
82C GLU* 2.8 28.8 + - - +
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Residues in contact with GLU 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ARG* 3.6 29.8 + - - +
15C GLN 3.0 6.9 + - - -
16C LYS* 3.1 41.0 + - + +
17C VAL 3.0 20.8 + - - +
38C VAL* 3.7 14.1 - - + +
39C VAL* 1.3 79.7 - - - +
41C PHE* 1.3 70.2 + - - +
82C GLU* 3.4 21.8 - - + +
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Residues in contact with PHE 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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17C VAL* 2.7 55.4 - - + -
19C LEU* 3.4 39.9 - - + -
26C HIS* 4.2 12.8 - + - -
39C VAL* 3.3 35.4 - - + -
40C GLU* 1.3 95.6 - - - +
42C THR* 1.3 63.7 + - - +
73C MET* 4.1 22.9 - - + -
74C VAL 4.7 5.6 - - - -
75C VAL* 4.7 5.4 - - + -
81C LEU* 4.8 7.9 - - + -
82C GLU 3.0 8.3 + - - +
83C LEU* 3.1 12.1 - - + +
84C THR 3.0 21.7 + - - -
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Residues in contact with THR 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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17C VAL 5.1 1.8 + - - -
19C LEU* 4.2 5.5 - - - +
41C PHE* 1.3 73.7 - - - +
43C MET* 1.3 71.8 + - - +
44C VAL* 5.0 4.0 - - + +
65C ASN* 4.2 4.2 - - - +
84C THR* 3.1 35.2 + - + +
86C ILE* 3.9 23.3 - - + -
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Residues in contact with MET 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C LEU* 3.5 16.2 - - + -
42C THR* 1.3 84.9 - - - +
44C VAL* 1.3 63.4 + - - +
64C PHE* 4.2 20.0 - - + -
65C ASN* 3.6 19.3 - - - +
71C PRO* 3.4 34.1 - - + -
73C MET* 3.6 31.0 - - + -
83C LEU* 3.9 21.7 - - + +
84C THR 3.2 5.2 + - - -
85C LEU* 2.8 28.5 - - + +
86C ILE 3.3 8.2 + - - -
97C ILE* 4.4 10.1 - - + -
134C TYR* 5.2 2.7 - - + -
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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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42C THR* 5.0 4.3 - - + -
43C MET* 1.3 74.8 - - - +
45C ILE* 1.3 63.2 + - - +
46C GLU* 3.7 19.0 + - + +
65C ASN* 2.8 27.7 + - - +
66C GLY 4.0 1.0 + - - -
86C ILE* 3.4 33.7 - - + +
88C PRO* 3.1 35.7 - - + -
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Residues in contact with ILE 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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44C VAL* 1.3 72.5 - - - +
46C GLU* 1.3 67.3 + - - +
47C GLU* 4.7 1.6 - - + -
63C ALA 3.4 18.8 - - - +
64C PHE* 2.7 41.1 - - + -
85C LEU* 3.2 26.5 - - + -
86C ILE 3.1 13.3 + - - +
87C ASN* 4.4 11.4 - - + +
88C PRO* 3.2 10.7 - - - +
91C ASN* 2.8 25.0 + - - +
95C HIS* 4.0 24.2 - - + +
114C ILE* 4.6 0.4 - - + -
150C MET* 3.5 23.3 - - + -
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Residues in contact with GLU 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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44C VAL* 3.8 25.5 - - + +
45C ILE* 1.3 82.5 - - - +
47C GLU* 1.3 63.7 + - - +
48C LYS* 3.4 19.2 + - + +
61C ALA 3.6 1.0 - - - +
63C ALA* 2.9 29.8 + - - +
65C ASN 5.2 0.4 - - - -
66C GLY* 4.3 20.2 - - - +
88C PRO* 4.3 8.0 - - - +
90C THR* 4.5 7.8 + - - -
91C ASN* 4.1 2.1 - - - +
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Residues in contact with GLU 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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45C ILE* 4.7 2.0 - - + -
46C GLU* 1.3 71.5 - - - +
48C LYS* 1.3 60.0 + - - +
60C HIS* 5.9 1.3 - - - -
61C ALA 3.1 9.6 - - - +
62C MET* 4.2 17.7 - - + +
91C ASN* 3.1 29.0 + - - +
92C THR* 3.2 26.4 + - - +
93C LEU* 3.4 21.2 + - - +
95C HIS* 2.0 44.3 + - - +
199C PRO* 4.7 11.6 - - + +
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Residues in contact with LYS 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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46C GLU* 4.1 21.7 - - + +
47C GLU* 1.3 74.8 - - - +
49C LYS* 1.3 70.4 + - - +
50C ILE* 4.5 19.0 - - + +
60C HIS* 3.4 8.0 - - - +
61C ALA* 2.8 29.4 + - + +
63C ALA* 6.1 1.8 - - + -
66C GLY* 3.6 28.2 + - - -
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Residues in contact with LYS 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 LYS* 1.3 84.6 - - - +
50C ILE* 1.3 62.7 + - - +
51C VAL* 4.4 1.8 + - - +
58C GLU* 3.7 32.5 + - + +
59C VAL 3.8 3.4 - - - +
60C HIS* 2.5 54.5 - - + +
195C LYS* 4.7 1.4 - - - +
196C TYR 2.2 33.3 + - - +
197C GLU* 3.8 11.8 + - - +
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Residues in contact with ILE 50 (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 LYS* 4.5 18.8 - - + -
49C LYS* 1.3 80.1 - - - +
51C VAL* 1.3 66.0 + - - +
52C ILE* 3.7 9.6 + - + +
58C GLU* 3.4 2.5 - - - -
59C VAL* 3.0 37.8 + - + +
61C ALA* 3.7 25.1 - - + -
68C VAL* 4.5 15.0 - - + -
183C PHE* 4.6 9.4 - - + -
222C GLY* 3.9 26.7 - - - +
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Residues in contact with VAL 51 (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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49C LYS 5.6 0.9 - - - +
50C ILE* 1.3 76.7 - - - +
52C ILE* 1.3 65.0 + - - +
53C ASP 3.3 22.4 - - - +
56C GLY* 3.8 15.0 - - - +
57C THR 3.2 12.6 - - - +
58C GLU* 4.2 18.6 - - + +
222C GLY 3.7 10.9 - - - +
223C ALA* 3.8 7.1 - - - +
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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