Contacts of the strand formed by residues 58 - 64 (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 GLU 58 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49C LYS* 3.7 37.9 + - + +
50C ILE 3.4 7.0 - - - +
51C VAL* 4.2 16.5 - - + +
56C GLY* 3.1 16.0 + - - +
57C THR* 1.3 81.7 - - - +
59C VAL* 1.3 67.1 + - - +
60C HIS* 4.3 3.4 + - - -
185C VAL* 4.6 6.8 - - - +
194C LYS 4.8 6.6 + - - +
195C LYS* 3.4 37.4 - - + +
196C TYR* 6.1 0.9 - - - -
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Residues in contact with VAL 59 (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* 4.6 1.6 - - - -
50C ILE* 3.0 30.3 + - + +
52C ILE* 4.1 21.7 - - + +
58C GLU* 1.3 75.8 - - - +
60C HIS* 1.3 64.8 + - - +
61C ALA* 2.7 21.7 + - - +
148C SER* 4.6 4.9 - - - +
183C PHE* 3.9 35.9 - - + -
184C TYR 5.9 0.4 - - - -
185C VAL* 3.6 31.6 - - + -
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Residues in contact with HIS 60 (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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47C GLU* 5.9 1.2 - - - -
48C LYS* 3.4 10.5 + - - +
49C LYS* 2.5 47.0 + - + +
58C GLU 5.4 2.2 - - - -
59C VAL* 1.3 72.3 - - - +
61C ALA* 1.3 63.2 + - - +
62C MET* 4.3 5.2 - - + +
144C TRP* 6.0 1.3 - - + -
148C SER* 3.7 18.2 + - - -
196C TYR* 4.0 12.3 - + + -
197C GLU 3.7 3.3 - - - -
198C ALA* 3.2 39.7 + - - -
199C PRO* 3.4 32.3 - - + +
202C ALA* 4.9 10.1 - - + -
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Residues in contact with ALA 61 (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 3.6 1.2 - - - +
47C GLU* 3.1 5.4 - - - +
48C LYS* 2.8 33.5 + - + +
50C ILE* 3.7 43.1 - - + -
59C VAL* 2.7 6.3 + - + -
60C HIS* 1.3 74.9 - - - +
62C MET* 1.3 61.9 + - - +
63C ALA* 3.8 3.1 - - + -
68C VAL* 4.1 11.4 - - + -
148C SER 3.2 14.6 - - - +
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Residues in contact with MET 62 (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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47C GLU* 4.2 15.5 - - + -
60C HIS 4.3 4.3 - - - +
61C ALA* 1.3 75.1 - - - +
63C ALA* 1.3 61.4 + - - +
93C LEU* 4.1 11.0 - - + -
95C HIS* 3.9 13.9 - - + -
144C TRP* 3.9 41.5 - - + -
145C HIS* 3.7 38.6 - - + -
148C SER* 3.2 26.6 + - - +
149C GLY 2.9 23.7 - - - +
150C MET* 3.3 25.4 - - + -
199C PRO* 5.0 4.7 - - + -
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Residues in contact with ALA 63 (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* 3.4 5.3 - - - +
46C GLU 2.9 43.1 + - - +
48C LYS* 6.1 2.2 - - + -
50C ILE* 6.4 0.7 - - + -
61C ALA* 4.8 4.3 - - + -
62C MET* 1.3 79.1 - - - +
64C PHE* 1.3 64.8 + - - +
66C GLY* 3.4 9.0 + - - -
67C THR* 3.6 23.8 - - - +
68C VAL* 3.9 19.1 - - + -
149C GLY 4.2 2.5 - - - -
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Residues in contact with PHE 64 (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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43C MET* 4.2 19.1 - - + -
44C VAL 4.1 0.7 - - - -
45C ILE* 2.7 42.4 - - + -
62C MET 4.1 0.2 + - - -
63C ALA* 1.3 73.3 - - - +
65C ASN* 1.3 71.8 + - - +
66C GLY 3.3 0.3 + - - -
67C THR 3.6 5.9 + - - -
70C GLY* 3.6 24.1 - - - -
85C LEU* 3.2 26.0 - - + -
96C ASN 3.9 14.4 - - - -
97C ILE* 4.4 12.6 - - + -
134C TYR* 4.3 16.4 - + + -
135C HIS 4.9 0.7 - - - -
136C CYS* 3.7 11.9 - - + -
149C GLY 4.9 1.8 + - - -
150C MET* 2.7 52.3 - - + -
151C ASN 4.7 0.9 - - - +
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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