Contacts of the strand formed by residues 286 - 294 (chain B) in PDB entry 4H1S
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 TYR 286 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B THR* 4.4 12.1 - - - +
247B PHE* 3.5 30.9 - + - -
254B PRO* 3.9 13.3 - - + +
255B SER* 3.5 14.2 + - - -
257B GLU* 2.6 30.5 + - - +
280B ALA* 4.3 17.1 + - + +
281B TYR* 4.0 22.7 - + + -
282B ALA 4.9 0.4 + - - -
284B GLY* 4.2 7.6 - - - -
285B LYS* 1.3 96.1 - - + +
287B LEU* 1.3 61.4 + - - +
288B GLY 4.0 0.9 + - - -
307B PRO* 3.8 27.8 - - + -
308B ILE 3.2 5.8 - - - +
309B LEU* 3.6 39.7 - - + -
310B LEU* 4.1 6.5 - - - +
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Residues in contact with LEU 287 (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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32B LEU* 4.1 12.1 - - + -
33B HIS 3.9 17.0 - - - +
34B THR* 4.1 6.5 - - + -
64B LEU* 3.7 26.0 - - + -
67B LYS* 4.0 22.7 - - + -
68B VAL* 4.1 16.8 - - + -
71B ILE* 4.0 18.6 - - + -
80B LEU* 4.3 6.1 - - + -
286B TYR* 1.3 71.6 - - - +
288B GLY* 1.3 78.0 + - - +
289B TYR 3.5 0.5 + - - -
307B PRO* 4.2 1.1 - - - -
308B ILE* 2.7 42.8 + - + +
310B LEU* 4.0 12.9 - - + +
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Residues in contact with GLY 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 3.2 8.1 - - - -
33B HIS* 2.8 64.4 + - - -
263B TYR* 4.0 1.3 - - - -
280B ALA* 3.8 10.2 - - - +
287B LEU* 1.3 78.8 - - - +
289B TYR* 1.3 58.6 + - - +
307B PRO* 4.2 5.2 - - - -
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Residues in contact with TYR 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B THR* 3.7 15.5 - - + -
31B ILE 3.5 2.9 - - - -
32B LEU* 3.5 19.5 - - + -
71B ILE* 3.9 22.9 - - + -
75B GLU* 2.6 25.6 + - - -
263B TYR* 3.0 11.7 + - - -
287B LEU 3.5 1.0 + - - -
288B GLY* 1.3 72.9 - - - +
290B LEU* 1.3 57.5 + - - +
291B LYS* 3.1 33.1 - - + -
304B HIS* 5.5 2.9 - + - -
305B GLY* 3.3 12.8 - - - -
306B ASN 3.0 39.7 + - - +
308B ILE* 3.9 19.7 - - + -
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Residues in contact with LEU 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU 3.5 1.7 - - - +
30B THR* 3.5 2.4 - - - -
31B ILE* 2.8 54.4 + - + +
33B HIS* 5.0 0.4 - - - +
238B VAL* 4.0 27.6 - - + -
263B TYR* 3.4 21.8 - - + +
264B PRO* 4.0 14.8 - - + -
276B PRO* 4.4 12.1 - - + -
278B VAL* 4.1 17.3 - - + -
289B TYR* 1.3 76.2 - - - +
291B LYS* 1.3 64.8 + - - +
292B ILE* 4.0 5.3 + - + -
303B SER* 4.0 15.9 - - - -
304B HIS 3.6 22.2 - - - +
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Residues in contact with LYS 291 (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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28B GLU* 2.5 41.9 + - - +
29B LEU 3.5 2.2 - - - -
30B THR* 3.0 21.7 + - - +
75B GLU* 2.9 25.4 + - - -
76B PRO* 6.0 0.4 - - - +
289B TYR* 3.1 34.0 - - + +
290B LEU* 1.3 71.9 - - - +
292B ILE* 1.3 63.0 + - - +
293B GLU* 5.4 1.5 - - - +
303B SER* 3.1 5.4 - - - -
304B HIS* 2.7 62.9 + - + +
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Residues in contact with ILE 292 (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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27B TRP 3.7 1.0 - - - +
28B GLU* 3.3 6.0 - - - +
29B LEU* 2.8 63.0 + - + +
31B ILE* 4.4 13.0 - - + -
238B VAL* 3.6 16.2 - - + -
276B PRO* 4.9 2.2 - - + -
290B LEU* 4.5 7.4 - - + +
291B LYS* 1.3 76.3 - - - +
293B GLU* 1.3 66.1 + - - +
294B PHE* 3.3 34.0 + - + -
300B VAL* 3.4 32.5 - - + -
302B SER 3.5 8.5 - - - +
303B SER* 4.2 5.6 - - - -
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Residues in contact with GLU 293 (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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27B TRP 3.9 3.6 + - - +
28B GLU* 3.1 45.6 + - - +
291B LYS 5.4 0.9 - - - +
292B ILE* 1.3 72.1 - - - +
294B PHE* 1.3 59.1 + - - +
300B VAL* 3.6 4.5 - - - -
301B ILE* 2.8 39.9 + - + -
302B SER* 2.9 35.2 + - - +
303B SER* 5.7 0.2 - - - -
304B HIS* 5.8 5.5 - - - +
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Residues in contact with PHE 294 (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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27B TRP* 2.9 54.8 + + + +
29B LEU* 3.9 26.0 - - + -
171B VAL* 6.0 0.2 - - + -
214B LYS* 3.6 41.3 - - + +
215B ILE 6.3 0.2 - - - -
216B ILE* 6.0 3.6 - - + -
237B ASP* 4.0 17.5 - - + -
238B VAL* 4.8 2.7 - - + -
292B ILE* 3.3 42.8 - - + -
293B GLU* 1.3 75.1 - - - +
295B ASP* 1.3 66.9 + - - +
298B GLY 3.8 13.9 - - - -
299B ASN 3.4 6.5 - - - -
300B VAL* 3.9 10.3 - - + -
301B ILE* 4.3 3.4 - - - -
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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
------------------------------------------------------------
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