Contacts of the strand formed by residues 310 - 330 (chain B) 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 GLU 310 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B THR* 3.8 16.1 - - - +
116B GLN* 4.7 4.6 + - + +
167B TRP* 3.6 24.0 - - + -
302B TYR* 4.0 14.3 - - - +
303B TYR 4.0 7.9 - - - +
304B LYS* 5.0 2.7 - - + +
308B GLY 4.0 1.4 + - - +
309B THR* 1.3 75.4 - - - +
311B THR* 1.3 68.4 + - - +
92C TYR* 3.9 10.9 + - - -
301C LYS* 3.7 15.1 + - - -
303C TYR* 2.9 31.5 + - + +
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Residues in contact with THR 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ASN* 4.6 15.5 - - - +
114B GLN 3.1 10.8 - - - -
115B THR* 3.4 19.1 - - + -
167B TRP* 4.6 2.9 - - - -
302B TYR* 3.7 2.5 - - - +
303B TYR* 2.9 52.4 + - - +
305B ASN* 4.4 22.3 - - + +
309B THR* 4.5 2.5 - - - +
310B GLU* 1.3 81.0 - - - +
312B ARG* 1.3 63.6 + - - +
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Residues in contact with ARG 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ASN* 3.9 2.6 + - - -
114B GLN* 2.7 58.6 + - + +
167B TRP* 3.2 48.6 - - + +
300B ALA* 3.9 7.0 - - + -
301B LYS 3.1 12.1 - - - +
302B TYR* 3.6 32.7 + - + -
303B TYR* 4.9 2.2 - - - -
311B THR* 1.3 76.1 - - - +
313B THR* 1.3 62.5 + - - +
314B LEU* 3.1 24.2 - - - +
88C ASP* 2.5 43.4 + - - -
91C ASP* 3.7 14.4 - - - +
92C TYR* 4.2 1.0 - - - +
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Residues in contact with THR 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ILE* 3.9 22.9 - - + -
111B THR 3.5 11.7 - - - +
112B THR* 4.0 17.3 - - + +
113B ASN 4.5 2.3 + - - -
300B ALA* 3.3 7.9 - - - -
301B LYS* 2.9 40.4 + - + -
303B TYR* 3.6 18.8 + - - +
312B ARG* 1.3 71.6 + - - +
314B LEU* 1.3 62.0 + - - +
315B ILE* 3.7 16.1 + - + +
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Residues in contact with LEU 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ILE 4.0 0.7 - - - +
110B ILE* 3.7 0.3 - - - -
111B THR* 2.7 43.9 + - - +
114B GLN* 3.3 30.5 - - - +
171B GLU* 4.1 23.6 - - + +
298B ARG* 3.9 32.8 - - + +
299B PHE 3.4 12.1 - - - +
300B ALA* 4.6 1.1 - - - -
312B ARG* 3.1 31.7 + - - +
313B THR* 1.3 72.9 - - - +
315B ILE* 1.3 71.8 + - - +
316B LYS 4.2 0.2 - - - -
88C ASP* 4.3 4.0 - - - +
91C ASP* 4.0 9.0 - - + -
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Residues in contact with ILE 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B TRP* 5.6 5.4 - - + -
92B TYR* 5.2 7.4 - - + +
108B MET* 4.6 18.4 - - + -
109B ILE 4.0 2.5 - - - -
110B ILE* 4.6 18.6 - - + +
297B PHE 3.6 0.3 - - - +
298B ARG* 3.3 3.6 - - - -
299B PHE* 2.9 74.1 + - + +
301B LYS* 4.5 18.2 - - + +
313B THR* 3.8 23.6 - - + +
314B LEU* 1.3 81.3 - - - +
316B LYS* 1.3 61.5 + - - +
317B GLY* 3.3 14.5 + - - +
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Residues in contact with LYS 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B MET* 3.3 3.8 - - - -
109B ILE* 3.1 40.3 + - + +
171B GLU* 3.8 26.4 + - - +
296B ASN* 4.9 7.6 - - - +
297B PHE 3.7 5.8 - - - -
298B ARG* 4.6 13.5 - - + +
314B LEU* 4.2 1.8 - - - +
315B ILE* 1.3 69.6 - - - +
317B GLY* 1.3 59.9 + - - +
318B TYR* 3.6 16.7 - - + +
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Residues in contact with GLY 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B PHE* 4.4 5.6 - - - -
105B LEU* 3.7 15.7 - - - -
107B ASN 3.7 7.0 - - - -
108B MET* 4.5 0.7 - - - -
296B ASN* 3.1 4.2 - - - +
297B PHE* 2.9 36.5 + - - +
299B PHE* 4.7 5.1 - - - -
315B ILE* 3.3 12.2 + - - -
316B LYS* 1.3 71.8 - - - +
318B TYR* 1.3 63.7 + - - -
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Residues in contact with TYR 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B PHE* 4.1 1.3 - - - -
105B LEU* 3.1 5.6 - - - +
106B THR* 3.0 16.5 + - - +
107B ASN* 2.8 34.3 + - + +
108B MET 4.1 0.9 - - - -
109B ILE* 3.6 24.9 - - + +
174B VAL 5.1 0.7 + - - -
176B PRO* 3.6 33.3 - - + +
251B VAL 3.8 15.5 - - - +
252B ARG* 3.4 35.7 - - + -
253B GLY 4.4 0.4 - - - +
295B TYR 3.6 3.8 - - - -
296B ASN* 3.5 26.1 + - + -
316B LYS* 3.6 22.8 - - + +
317B GLY* 1.3 74.3 - - - -
319B GLY* 1.3 58.7 + - - +
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Residues in contact with GLY 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B PHE* 3.6 12.4 - - - -
104B VAL 3.3 11.4 - - - -
106B THR* 2.9 15.0 + - - -
253B GLY* 3.1 20.6 - - - -
254B GLY 3.1 6.2 + - - +
295B TYR* 3.3 12.4 + - - +
318B TYR* 1.3 76.1 - - - +
320B ILE* 1.3 65.6 + - - -
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Residues in contact with ILE 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B PHE* 4.0 2.5 - - - -
104B VAL* 3.2 27.9 + - + +
106B THR* 4.3 9.6 - - + +
239B VAL* 4.3 3.8 - - + -
246B PHE* 3.4 46.7 - - + -
249B MET* 4.0 25.1 - - + -
250B ALA* 4.5 11.7 - - + +
254B GLY 3.1 11.7 - - - +
256B MET* 3.7 30.5 - - + +
319B GLY* 1.3 75.3 - - - -
321B ARG* 1.3 62.5 + - - +
322B PHE* 3.5 20.1 - - + -
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Residues in contact with ARG 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B SER* 4.5 8.3 - - - -
102B PHE* 3.6 12.1 - - - +
103B PHE* 4.0 15.2 - - + -
254B GLY 2.9 8.1 + - - -
255B VAL* 3.2 19.3 - - + +
256B MET 2.9 24.5 + - - +
295B TYR* 3.3 38.5 + - + +
319B GLY 4.0 1.2 + - - -
320B ILE* 1.3 71.5 - - - +
322B PHE* 1.3 62.1 + - - +
323B ASP* 2.7 54.3 + - - -
66C SER* 4.5 0.4 + - - -
67C VAL 2.9 27.1 + - - -
68C THR* 3.2 18.7 + - - +
99C ASP* 3.9 29.0 + - - +
100C GLY 5.2 0.2 - - - +
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Residues in contact with PHE 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B SER* 3.1 6.6 - - - -
102B PHE* 2.7 74.2 + + + -
104B VAL* 3.9 15.5 - - + -
235B LEU* 3.6 28.7 - - + -
238B ILE* 3.7 31.2 - - + -
239B VAL* 4.8 2.5 - - + -
246B PHE* 4.8 1.8 - + - -
256B MET* 3.5 21.5 - - + +
258B VAL* 4.3 12.8 - - + -
320B ILE* 3.5 41.3 - - + -
321B ARG* 1.3 71.9 - - - +
323B ASP* 1.3 61.8 + - - +
324B VAL* 3.7 1.1 + - + -
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Residues in contact with ASP 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B SER* 3.4 13.7 + - - +
255B VAL* 5.4 2.9 - - - +
256B MET 2.9 13.0 + - - +
257B GLY* 3.6 1.9 - - - -
258B VAL* 2.9 26.5 + - - -
282B LEU* 4.4 9.2 - - + -
321B ARG* 2.7 53.9 + - - -
322B PHE* 1.3 69.4 - - - +
324B VAL* 1.3 61.9 + - - +
325B MET* 3.3 18.8 + - + +
66C SER* 2.9 23.6 + - - +
67C VAL 4.9 0.2 + - - -
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Residues in contact with VAL 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B VAL* 3.7 37.1 - - + +
69B THR* 4.4 22.2 - - + -
100B GLY* 4.5 9.3 - - - +
101B SER* 3.9 8.0 + - - +
102B PHE* 4.7 9.2 - - + -
192B ILE* 4.5 15.7 - - + -
258B VAL* 3.5 17.3 - - + +
260B ILE* 4.1 15.5 - - + -
322B PHE 3.7 2.0 + - - +
323B ASP* 1.3 69.9 - - - +
325B MET* 1.3 60.3 + - - +
326B VAL* 3.7 13.3 + - + +
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Residues in contact with MET 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257B GLY* 3.3 34.1 - - - -
258B VAL 3.0 9.2 + - - +
259B GLN* 3.3 34.4 - - + +
260B ILE 2.9 24.5 + - - +
282B LEU* 3.9 21.5 - - + -
323B ASP* 3.3 11.0 + - + +
324B VAL* 1.3 73.0 - - - +
326B VAL* 1.3 62.9 + - - +
327B PHE* 4.0 3.7 + - - -
64C LEU* 4.3 26.2 - - + +
65C SER 4.1 21.3 - - - +
66C SER* 4.4 5.6 - - - -
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Residues in contact with VAL 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B VAL* 4.9 2.5 - - + -
65B SER* 3.1 37.2 - - - +
67B VAL* 3.8 19.7 - - + -
194B ASN* 3.5 24.9 - - - +
196B ILE* 4.1 2.9 - - + -
260B ILE* 3.5 11.9 - - + +
262B TRP* 3.8 20.0 - - + +
324B VAL* 3.7 11.7 + - + +
325B MET* 1.3 74.2 - - - +
327B PHE* 1.3 70.1 + - - +
64C LEU* 5.1 3.5 - - - +
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Residues in contact with PHE 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B VAL* 4.2 10.8 - - - -
259B GLN* 4.3 22.2 - - + -
260B ILE 3.0 19.9 + - - +
261B ARG* 3.1 44.1 - - + -
262B TRP* 2.9 23.2 + - - -
263B ASP* 5.5 0.2 - - - -
325B MET 4.1 4.3 - - - -
326B VAL* 1.3 82.1 - - - +
328B GLY* 1.3 62.9 + - - +
64C LEU* 3.4 39.7 - - + -
197C ARG* 5.4 2.5 - - - -
199C PRO* 4.0 27.8 - - + -
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Residues in contact with GLY 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B THR* 3.4 11.1 - - - +
63B VAL* 3.4 29.7 + - - +
262B TRP 3.1 12.6 - - - -
263B ASP* 3.6 8.7 - - - -
327B PHE* 1.3 85.9 - - - +
329B GLN* 1.3 61.8 + - - +
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Residues in contact with GLN 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B THR* 5.5 6.3 - - - -
61B ASP 3.3 14.8 - - - +
62B THR* 5.2 2.9 - - + -
198B TYR* 3.9 2.9 + - - -
262B TRP 3.0 14.3 + - - +
263B ASP* 3.3 13.6 + - - +
264B CYS 3.2 13.9 + - - +
328B GLY* 1.3 75.8 - - - +
330B ALA* 1.3 62.8 + - - +
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Residues in contact with ALA 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B GLN* 5.2 0.9 - - - -
59B ASP 3.3 4.2 - - - +
60B THR* 3.5 3.5 - - - -
61B ASP 3.1 26.4 + - - -
198B TYR* 3.6 24.2 - - + +
201B PHE* 3.6 5.6 - - + -
264B CYS 3.2 19.5 - - - +
266B LEU* 3.5 22.7 - - + -
329B GLN* 1.3 78.0 - - - +
331B GLY* 1.3 59.0 + - - +
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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
------------------------------------------------------------
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