Contacts of the helix formed by residues 307 - 324 (chain B) in PDB entry 1SVU
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 VAL 307 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B ALA* 3.6 29.4 - - + -
159B ILE* 3.6 35.0 - - + -
161B GLN* 5.2 1.3 - - - +
163B ARG* 3.7 24.7 - - + -
165B ARG* 5.4 0.4 - - + -
167B TYR* 4.3 9.0 - - - +
283B MET* 3.8 17.7 - - - -
306B VAL* 1.3 75.0 - - + +
308B ILE* 1.3 67.5 + - - +
309B ASN 4.4 3.6 - - - +
310B VAL* 3.1 14.8 + - + +
311B LEU* 3.0 20.2 + - - +
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Residues in contact with ILE 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 3.4 44.0 - - + -
23B GLY* 3.5 29.8 - - - +
26B LEU* 4.6 5.4 - - + -
27B ALA* 4.5 5.4 - - + +
283B MET 3.5 4.3 + - - +
284B GLY 3.8 12.8 - - - +
285B TYR* 3.6 37.9 - - + +
286B PRO* 5.5 0.4 - - + -
306B VAL 3.1 16.1 + - - +
307B VAL* 1.3 69.6 - - - +
309B ASN* 1.3 54.5 + - - +
310B VAL 2.9 0.5 + - - -
311B LEU* 2.9 7.5 + - + +
312B GLN* 2.5 44.6 + - + +
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Residues in contact with ASN 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 3.2 29.5 - - - -
2B ILE* 3.4 25.2 + - - +
157B TYR 3.8 18.5 + - - +
158B GLY* 4.8 5.3 + - - -
159B ILE* 3.8 30.8 - - + +
284B GLY* 3.8 6.5 - - - +
307B VAL* 4.4 1.0 - - + +
308B ILE* 1.3 77.1 - - - +
310B VAL* 1.3 60.4 + - + +
312B GLN* 3.3 9.2 - - - +
313B TYR* 2.8 37.6 + - - -
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Residues in contact with VAL 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B LEU* 4.5 5.2 - - + -
154B ALA* 3.9 19.3 - - - +
157B TYR* 3.6 34.5 - - + -
159B ILE* 6.0 0.2 - - + -
167B TYR* 3.1 44.6 - - + +
183B PRO* 5.8 0.4 - - + -
307B VAL* 3.1 15.3 + - + +
308B ILE 3.0 0.8 - - - -
309B ASN* 1.3 74.1 - - + +
311B LEU* 1.3 69.2 + - - +
312B GLN 2.8 2.4 + - - -
313B TYR* 3.0 17.9 + - - +
314B ILE* 3.1 26.8 + - + +
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Residues in contact with LEU 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B GLY* 3.7 6.7 - - - +
24B PHE* 3.4 58.1 - - + +
27B ALA* 3.9 10.5 - - + +
117B PHE* 4.1 17.7 - - + -
119B GLU* 5.0 1.1 - - + -
167B TYR* 4.0 22.4 - - + -
306B VAL* 3.2 36.3 - - + -
307B VAL 3.0 5.4 + - - +
308B ILE* 2.9 11.6 + - + +
310B VAL* 1.3 80.5 - - - +
312B GLN* 1.3 65.7 + - - +
314B ILE* 3.5 5.1 + - - +
315B ALA* 3.1 18.0 + - - +
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Residues in contact with GLN 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 3.1 11.3 - - - +
2B ILE* 2.7 62.3 + - + +
4B ILE* 3.1 32.4 - - + +
27B ALA* 3.7 18.1 - - + +
30B SER* 3.5 9.0 + - - +
31B CYS* 4.4 0.5 - - - -
308B ILE* 2.5 34.5 + - + +
309B ASN* 3.3 9.0 - - - +
310B VAL 2.8 0.6 + - - -
311B LEU* 1.3 69.7 - - - +
313B TYR* 1.3 69.1 - - - +
315B ALA* 2.7 24.4 + - - +
316B TYR* 3.1 4.1 + - - +
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Residues in contact with TYR 313 (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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327A TYR* 3.4 48.2 - + + -
2B ILE* 3.4 30.9 - - + +
157B TYR* 4.0 35.0 - + + -
183B PRO* 3.7 21.3 - - + -
186B PHE* 3.5 24.8 - + - -
309B ASN* 2.8 26.5 + - - -
310B VAL* 3.0 12.0 + - - +
312B GLN* 1.3 74.0 - - - +
314B ILE* 1.3 69.4 + - - +
316B TYR* 2.9 5.0 + - - +
317B ASN* 2.7 23.0 + - - +
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Residues in contact with ILE 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B PHE* 3.3 31.6 - - + -
152B LEU* 4.3 7.9 - - + -
167B TYR* 4.7 10.8 - - + -
169B ILE* 3.9 14.1 - - + -
180B PHE* 4.5 6.7 - - + -
182B PHE* 4.5 13.2 - - + -
183B PRO* 3.9 25.1 - - + +
310B VAL* 3.1 43.5 + - + +
311B LEU* 3.5 7.2 - - - +
313B TYR* 1.3 74.5 - - - +
315B ALA* 1.3 60.8 + - - +
317B ASN* 2.4 35.9 + - - +
318B ILE* 2.5 19.3 + - + -
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Residues in contact with ALA 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU* 4.4 2.4 - - + +
27B ALA 4.7 1.1 - - - +
28B LEU* 3.8 24.9 - - + -
31B CYS* 3.3 24.7 - - + -
117B PHE* 5.1 1.3 - - + -
311B LEU 3.1 8.8 + - - +
312B GLN* 2.7 19.1 + - - +
314B ILE* 1.3 76.5 - - - +
316B TYR* 1.3 50.9 + - - +
318B ILE* 2.7 16.0 + - - +
319B GLY* 2.5 34.5 + - - -
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Residues in contact with TYR 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A LYS* 2.7 36.5 + - - +
326A PRO* 4.1 3.1 - - + -
327A TYR* 3.4 38.1 - + + -
4B ILE* 3.5 25.8 - - + -
6B ASP* 3.1 48.8 + - + +
8B GLN* 3.1 28.3 + - + -
31B CYS* 4.0 7.6 - - - -
312B GLN 3.1 3.6 + - - +
313B TYR 2.9 12.1 + - - +
314B ILE 2.9 0.6 + - - -
315B ALA* 1.3 73.3 - - - +
317B ASN* 1.3 58.0 + - - +
318B ILE 2.7 4.0 + - - -
319B GLY* 2.8 3.5 + - - +
320B SER* 2.7 40.3 + - - -
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Residues in contact with ASN 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A PHE* 5.5 0.9 - - - -
326A PRO* 3.6 4.6 - - + +
327A TYR* 2.5 63.5 + - - +
180B PHE* 3.2 21.2 - - + -
181B GLN* 2.7 31.9 + - - +
183B PRO* 3.4 13.4 - - + -
313B TYR 2.7 10.5 + - - +
314B ILE* 2.4 19.2 + - - +
316B TYR* 1.3 70.9 - - - +
318B ILE* 1.3 55.7 + - - -
320B SER* 4.1 9.5 - - - -
321B SER* 3.7 11.3 + - - -
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Residues in contact with ILE 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU* 4.0 13.9 - - + -
28B LEU* 5.9 1.1 - - + -
74B ILE* 4.6 14.1 - - + -
115B VAL* 3.8 19.7 - - + -
117B PHE* 4.7 15.5 - - + -
169B ILE* 3.3 35.2 - - + -
171B PHE* 3.9 12.3 - - + -
180B PHE* 3.7 8.7 - - + -
314B ILE* 2.5 20.4 + - + +
315B ALA* 2.7 19.5 + - - +
317B ASN* 1.3 71.4 - - - +
319B GLY* 1.3 72.3 + - - +
320B SER 3.2 0.9 - - - -
321B SER* 3.3 8.8 + - - -
322B LEU* 3.1 23.9 + - + +
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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
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8B GLN* 3.0 33.4 - - - -
9B LEU* 3.4 11.0 - - - -
315B ALA 2.5 15.9 + - - -
316B TYR 3.5 1.8 - - - -
318B ILE* 1.3 74.7 - - - +
320B SER* 1.3 63.5 + - - +
322B LEU* 3.2 6.0 + - - +
323B ASN* 3.0 24.8 + - - -
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Residues in contact with SER 320 (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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324A PHE* 2.9 34.6 - - - -
325A LYS 3.5 17.3 + - - -
326A PRO* 3.9 4.6 - - - +
8B GLN* 3.2 28.8 + - - +
316B TYR* 2.7 24.6 + - - -
317B ASN* 4.1 9.2 - - - -
319B GLY* 1.3 71.7 - - - +
321B SER* 1.3 64.7 + - - +
323B ASN* 3.3 2.1 + - - +
324B PHE 3.3 12.6 + - - -
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Residues in contact with SER 321 (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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324A PHE* 3.5 4.4 - - - -
171B PHE* 4.3 3.8 - - - -
177B ILE* 2.9 35.4 - - - +
179B ASN* 2.7 31.5 + - - +
180B PHE* 3.0 26.0 - - - -
317B ASN 3.7 7.9 + - - -
318B ILE 3.3 9.7 + - - -
320B SER* 1.3 80.1 - - - +
322B LEU* 1.3 64.8 + - - +
324B PHE* 3.1 8.5 + - - +
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Residues in contact with LEU 322 (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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9B LEU* 4.8 0.4 - - + -
12B LEU* 3.3 39.0 - - + -
74B ILE* 4.9 0.7 - - + -
114B LYS* 5.9 2.2 - - + -
115B VAL* 4.0 18.2 - - + -
171B PHE* 3.9 28.9 - - + -
175B LEU* 4.6 11.0 - - + -
177B ILE* 3.7 14.8 - - + +
318B ILE* 3.1 21.8 - - + +
319B GLY* 3.2 6.0 + - - +
321B SER* 1.3 76.3 - - - +
323B ASN* 1.3 64.5 + - - +
324B PHE 3.0 10.2 + - - +
325B LYS* 4.4 5.7 + - - +
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Residues in contact with ASN 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A GLN* 4.6 10.4 - - - +
316A TYR* 5.5 1.9 + - - -
320A SER* 4.7 1.7 + - - -
324A PHE* 5.8 0.2 - - - -
8B GLN* 3.0 49.4 + - - +
12B LEU* 6.0 1.0 - - - +
319B GLY* 3.0 12.3 + - - +
320B SER 3.3 1.7 + - - +
322B LEU* 1.3 81.2 - - - +
324B PHE* 1.3 57.9 + - - +
325B LYS* 3.0 9.9 + - - +
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Residues in contact with PHE 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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179A ASN* 2.9 46.0 - - + -
181A GLN* 4.8 5.2 - - + -
317A ASN 5.5 0.4 - - - -
320A SER* 3.0 38.8 - - - -
321A SER* 4.2 1.8 - - - -
324A PHE* 4.1 14.1 - + + -
177B ILE* 5.1 3.5 - - - +
179B ASN* 3.3 32.5 - - + +
320B SER 3.3 8.4 + - - +
321B SER 3.1 7.7 + - - +
322B LEU 3.0 5.8 + - - +
323B ASN* 1.3 75.9 - - - +
325B LYS* 1.3 57.0 + - - +
326B PRO* 3.4 33.8 - - + +
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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
------------------------------------------------------------
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