Contacts of the strand formed by residues 58 - 64 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A LYS* 4.7 27.3 + - + +
50A ILE 3.4 8.3 - - - +
51A VAL* 4.1 16.0 - - + +
52A ILE* 5.4 0.2 - - - -
56A GLY 3.1 14.1 - - - +
57A THR* 1.3 81.1 - - - +
59A VAL* 1.3 69.0 + - - +
60A HIS* 4.3 4.5 + - + -
185A VAL* 4.6 6.8 - - - +
193A TYR* 5.6 0.4 - - - +
194A LYS 4.8 6.4 + - - +
195A LYS* 3.3 51.4 + - + +
196A TYR* 6.2 0.2 - - - -
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Residues in contact with VAL 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LYS* 4.6 1.3 - - - -
50A ILE* 3.0 30.4 + - + +
52A ILE* 4.1 22.1 - - + +
58A GLU* 1.3 77.0 - - - +
60A HIS* 1.3 62.9 + - - +
61A ALA* 2.6 23.2 + - + +
148A SER* 4.6 5.6 - - - +
183A PHE* 4.1 29.6 - - + -
184A TYR 5.8 0.4 - - - -
185A VAL* 3.4 34.3 - - + -
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Residues in contact with HIS 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A GLU* 6.2 1.0 - - + -
48A LYS* 3.5 11.2 + - - +
49A LYS* 3.1 40.4 - - + +
58A GLU* 5.5 3.4 - - + -
59A VAL* 1.3 71.1 - - - +
61A ALA* 1.3 63.9 + - - +
62A MET* 3.8 6.0 + - + +
144A TRP* 6.0 1.7 - - + -
148A SER* 3.9 16.5 + - - -
196A TYR* 3.4 27.5 + + + -
197A GLU 3.4 20.0 - - - -
198A ALA* 3.5 18.7 + - - -
199A PRO* 3.7 31.6 - - + +
202A ALA* 5.4 5.2 - - + -
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Residues in contact with ALA 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A GLU 3.6 1.3 - - - +
47A GLU* 3.2 6.4 - - - +
48A LYS* 2.8 35.6 + - + +
50A ILE* 3.8 31.2 - - + -
59A VAL* 2.6 14.3 + - + +
60A HIS* 1.3 74.4 - - - +
62A MET* 1.3 61.9 + - - +
63A ALA* 3.8 3.8 - - + -
68A VAL* 4.3 11.0 - - + -
148A SER 3.3 14.8 - - - +
183A PHE* 6.1 0.4 - - + -
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Residues in contact with MET 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ILE* 5.2 0.2 - - - -
46A GLU 4.1 2.2 - - - -
47A GLU* 4.4 11.4 - - + -
60A HIS 4.2 5.2 - - - +
61A ALA* 1.3 76.8 - - - +
63A ALA* 1.3 62.3 + - - +
93A LEU* 4.0 8.7 - - + -
95A HIS* 3.9 13.9 - - + -
144A TRP* 3.5 43.3 - - + -
145A HIS* 3.7 31.4 - - - -
148A SER* 3.3 32.9 + - - +
149A GLY 2.8 24.3 - - - +
150A MET* 3.3 25.3 - - + -
199A PRO* 4.8 4.5 - - + -
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Residues in contact with ALA 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ILE* 3.3 6.9 - - - +
46A GLU 2.9 43.2 + - - +
48A LYS* 5.6 3.6 - - - -
61A ALA* 5.0 3.8 - - + -
62A MET* 1.3 77.4 - - - +
64A PHE* 1.3 64.7 + - - +
65A ASN 3.4 0.7 + - - -
66A GLY* 3.5 6.7 + - - -
67A THR 3.6 23.8 - - - +
68A VAL* 3.8 19.1 - - + -
149A GLY 4.1 2.9 - - - -
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Residues in contact with PHE 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A MET* 4.4 16.6 - - + -
44A VAL 4.3 0.4 - - - -
45A ILE* 2.8 47.8 - - + -
62A MET 4.1 0.2 + - - -
63A ALA* 1.3 73.6 - - - +
65A ASN* 1.3 71.3 + - - +
66A GLY 3.3 0.3 + - - -
67A THR 3.6 8.8 + - - -
70A GLY* 3.6 14.7 - - - +
71A PRO* 3.6 7.4 - - - +
85A LEU* 3.4 24.0 - - + -
96A ASN 3.7 9.2 - - - -
97A ILE* 4.3 12.6 - - + -
134A TYR* 4.1 19.1 - + + -
135A HIS 4.7 0.4 - - - -
136A CYS* 3.6 21.8 - - + -
149A GLY 4.8 2.0 + - - -
150A MET* 2.7 46.0 - - + -
151A ASN 5.8 0.4 - - - +
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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