Contacts of the strand formed by residues 189 - 198 (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 THR 189 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A LYS 3.8 1.6 - - - +
71A VAL* 3.4 3.1 - - - -
72A LYS* 2.7 52.7 + - + +
187A ASN 4.9 3.1 - - - +
188A PHE* 1.3 81.0 - - - +
190A VAL* 1.3 57.1 + - - +
191A LEU 4.1 0.2 - - - -
221A VAL* 5.1 7.7 - - + +
232A ILE* 2.9 30.6 + - + +
233A PHE 3.1 14.5 + - - -
234A ARG* 4.0 5.9 + - - -
235A LEU* 4.4 1.3 - - - +
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Residues in contact with VAL 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A THR* 4.0 13.0 - - - -
70A LYS 3.6 3.4 - - - +
71A VAL* 3.7 26.0 - - + +
102A PHE* 3.7 19.1 - - + -
189A THR* 1.3 74.2 + - - +
191A LEU* 1.3 73.8 + - - +
192A ILE* 3.6 22.0 + - + +
231A PRO 3.6 0.7 - - - +
232A ILE* 3.6 3.0 - - - -
233A PHE* 2.8 38.2 + - + +
235A LEU* 4.1 17.5 - - + +
238A ILE* 4.2 9.2 - - + -
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Residues in contact with LEU 191 (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 3.5 1.0 - - - +
69A THR* 3.1 7.7 - - - -
70A LYS* 2.9 44.3 + - + +
189A THR 4.1 0.8 + - - -
190A VAL* 1.3 72.1 - - - +
192A ILE* 1.3 66.2 + - - +
193A LYS* 3.9 22.4 - - + -
208A ILE* 5.9 0.7 - - + -
231A PRO* 3.9 17.7 - - + +
232A ILE* 3.7 32.6 - - + +
291C VAL* 3.9 24.2 - - + -
292C ALA* 3.5 32.8 - - + -
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Residues in contact with ILE 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A VAL* 5.2 1.8 - - + -
68A THR 3.5 4.5 - - - +
69A THR* 4.4 5.8 - - + -
102A PHE* 5.2 2.5 - - + -
190A VAL* 3.8 28.0 - - + +
191A LEU* 1.3 79.0 - - - +
193A LYS* 1.3 61.4 + - - +
194A ASN* 5.2 0.4 - - + -
207A ASN* 2.7 29.8 + - - +
231A PRO* 3.2 18.0 + - - +
233A PHE* 3.8 25.3 - - + -
238A ILE* 5.1 0.9 - - + -
258A VAL* 4.3 24.2 - - + -
260A ILE* 4.3 22.4 - - + -
277A TYR* 5.8 0.4 - - + -
324A VAL* 4.5 22.0 - - + -
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Residues in contact with LYS 193 (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* 3.3 6.2 - - - +
68A THR* 2.8 54.5 + - + +
191A LEU* 3.9 24.9 - - + -
192A ILE* 1.3 77.0 - - - +
194A ASN* 1.3 59.9 + - - +
195A ASN 4.3 0.9 - - - -
207A ASN* 3.6 5.2 - - - +
208A ILE* 3.6 26.7 - - + -
231A PRO* 6.2 0.2 - - + -
283C ASP* 4.7 9.7 - - - +
284C ASN* 4.6 13.3 + - - +
290C ASN* 3.4 24.2 - - - +
291C VAL 3.5 18.6 + - - +
292C ALA* 4.0 12.8 + - + +
293C PRO* 5.1 0.8 - - - +
294C GLY 5.2 2.4 + - - +
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Residues in contact with ASN 194 (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* 3.2 17.2 + - - -
66A SER 2.9 20.7 + - - -
67A VAL* 3.7 12.2 - - + +
192A ILE* 5.2 0.4 - - + -
193A LYS* 1.3 76.7 - - - +
195A ASN* 1.3 64.3 + - - +
196A ILE* 3.4 4.9 + - - +
206A ARG* 3.5 3.5 - - - -
207A ASN* 2.6 47.2 + - + +
260A ILE* 3.8 14.9 - - + +
262A TRP* 3.0 28.6 + - - -
326A VAL* 3.5 14.0 - - - +
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Residues in contact with ASN 195 (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 3.9 0.5 - - - -
66A SER* 3.1 35.6 + - - +
193A LYS 4.3 0.6 - - - -
194A ASN* 1.3 74.3 + - - +
196A ILE* 1.3 87.1 + - - +
204A ASN* 4.6 2.6 - - - +
205A LYS 3.7 7.9 - - - +
206A ARG* 4.3 21.0 - - + +
280C ARG* 4.1 13.8 + - - +
281C ARG 4.7 1.0 + - - -
282C LEU* 2.8 60.3 + - + +
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Residues in contact with ILE 196 (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* 3.6 20.6 - - + -
64A LEU 3.5 3.6 - - - -
65A SER* 3.7 13.0 - - - +
194A ASN* 3.4 18.4 - - - +
195A ASN* 1.3 84.0 + - - +
197A ARG* 1.3 62.5 + - - +
198A TYR* 4.2 22.7 - - + -
203A PHE* 5.1 1.3 - - + -
204A ASN* 3.0 20.0 - - - +
205A LYS* 3.0 34.1 + - + +
262A TRP* 3.5 52.5 - - + +
273A CYS* 5.3 0.2 - - - -
280C ARG* 5.1 1.1 - - - +
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Residues in contact with ARG 197 (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* 4.0 3.0 - - - -
64A LEU* 3.0 38.9 + - + +
196A ILE* 1.3 77.7 - - - +
198A TYR* 1.3 66.3 + - - +
199A PRO* 3.5 5.7 - - + +
203A PHE 3.4 7.0 - - - +
204A ASN* 3.5 17.5 - - + +
259C GLN* 5.8 0.2 - - - +
280C ARG* 3.6 24.2 - - - +
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Residues in contact with TYR 198 (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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61A ASP* 3.3 37.5 - - + +
62A THR 3.9 8.1 - - - -
63A VAL* 3.5 22.1 - - + +
196A ILE* 4.2 13.7 - - + -
197A ARG* 1.3 71.9 - - - +
199A PRO* 1.3 70.7 - - - +
200A LYS 3.3 0.4 - - - -
201A PHE* 3.3 15.1 + + + -
202A ASN* 3.1 17.8 + - - -
203A PHE* 2.7 48.5 + + + +
262A TRP* 2.7 38.3 + - + +
264A CYS* 4.3 7.2 + - + +
266A LEU* 4.7 1.6 - - + -
329A GLN 3.7 3.1 + - - -
330A ALA* 3.7 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