Contacts of the strand formed by residues 64 - 72 (chain A) in PDB entry 3I5D
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 LEU 64 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A THR 3.8 1.8 + - - -
63A VAL* 1.3 73.3 - - - +
65A SER* 1.3 59.4 + - - +
195A ASN 4.3 0.2 - - - +
196A ILE* 3.5 4.7 - - - -
197A ARG* 3.0 43.8 + - + +
199A PRO* 4.6 14.1 - - + -
259C GLN* 6.5 1.8 - - + -
280C ARG* 5.5 3.0 + - - +
325C MET* 5.4 13.2 - - + -
327C PHE* 5.4 13.0 - - + -
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Residues in contact with SER 65 (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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63A VAL* 3.9 5.4 + - - -
64A LEU* 1.3 75.0 - - - +
66A SER* 1.3 72.2 + - - +
67A VAL* 4.2 1.2 - - - +
194A ASN* 3.2 11.8 + - - -
195A ASN 3.9 3.8 - - - -
196A ILE* 4.0 2.9 - - - -
326A VAL* 3.1 45.2 - - - +
325C MET* 4.0 16.0 - - - +
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Residues in contact with SER 66 (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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65A SER* 1.3 79.5 + - - +
67A VAL* 1.3 65.2 + - - +
68A THR* 5.5 0.7 + - - -
194A ASN* 2.9 15.2 + - - -
195A ASN* 3.1 27.4 + - - +
255C VAL* 5.1 3.8 - - - +
280C ARG* 6.1 0.7 - - - -
282C LEU* 3.6 27.9 - - - +
321C ARG* 4.6 0.3 + - - -
323C ASP* 3.0 24.8 + - - -
325C MET* 4.5 5.6 - - - -
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Residues in contact with VAL 67 (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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65A SER* 4.2 1.3 - - - +
66A SER* 1.3 79.4 + - - +
68A THR* 1.3 66.6 + - - +
69A THR* 5.4 0.7 - - + -
99A ASP 4.4 0.9 - - - +
100A GLY* 3.2 37.0 - - - +
192A ILE* 5.2 3.1 - - + -
193A LYS 3.3 8.7 - - - +
194A ASN* 3.7 19.7 - - + +
260A ILE* 5.1 0.2 - - + -
324A VAL* 3.6 34.5 - - + +
326A VAL* 3.8 11.2 - - + -
321C ARG* 2.8 25.5 + - - +
323C ASP* 4.9 1.0 + - - -
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Residues in contact with THR 68 (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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66A SER* 5.5 0.9 + - - -
67A VAL* 1.3 83.1 + - - +
69A THR* 1.3 73.7 + - - +
70A LYS* 5.9 0.9 - - + -
99A ASP 4.8 1.8 - - - -
191A LEU* 3.5 1.5 - - + +
192A ILE* 3.5 2.6 - - - +
193A LYS* 2.8 56.4 + - + +
255C VAL* 4.5 9.5 - - - +
292C ALA* 6.5 0.7 - - + -
295C TYR* 3.9 28.2 - - + -
321C ARG* 3.2 13.3 + - - +
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Residues in contact with THR 69 (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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67A VAL* 5.4 1.1 - - + -
68A THR* 1.3 88.5 - - - +
70A LYS* 1.3 63.4 + - - +
71A VAL* 5.5 0.8 - - - +
98A GLU 4.9 3.1 + - - -
99A ASP 4.3 6.9 + - - -
100A GLY 3.6 25.0 + - - +
102A PHE* 3.8 33.5 - - + +
190A VAL* 4.0 11.2 - - + -
191A LEU* 3.1 8.5 - - - +
192A ILE* 4.4 7.4 - - + -
324A VAL* 4.3 12.3 - - + -
295C TYR* 5.7 1.9 - - - -
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Residues in contact with LYS 70 (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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68A THR* 5.9 1.3 - - + -
69A THR* 1.3 76.2 - - - +
71A VAL* 1.3 64.8 + - - +
72A LYS* 3.8 2.6 + - - +
189A THR 3.8 0.3 - - - +
190A VAL* 3.6 0.5 - - - -
191A LEU* 2.9 48.6 + - + +
292C ALA* 5.4 7.0 - - + -
296C ASN 5.6 6.5 - - - +
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Residues in contact with VAL 71 (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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69A THR* 5.5 0.7 - - - +
70A LYS* 1.3 73.2 - - - +
72A LYS* 1.3 66.2 + - - +
89A VAL* 3.7 37.1 - - + +
90A ALA* 4.5 13.0 - - - +
94A ILE* 3.6 18.5 - - + +
102A PHE* 3.5 39.3 - - + -
104A VAL* 4.7 4.5 - - + -
188A PHE* 4.4 9.9 - - + -
189A THR 3.4 8.5 - - - +
190A VAL* 3.7 14.6 - - + -
235A LEU* 5.0 2.5 - - + -
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Residues in contact with LYS 72 (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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70A LYS 3.8 1.8 + - - +
71A VAL* 1.3 75.2 - - - +
73A GLY* 1.3 58.5 + - - +
89A VAL* 3.7 3.8 - - - -
90A ALA* 6.2 0.4 - - - -
188A PHE* 3.6 3.3 - - - +
189A THR* 2.7 50.6 + - + +
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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