Contacts of the strand formed by residues 180 - 192 (chain B) in PDB entry 3S9L
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 LYS 180 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178B LEU 3.2 2.1 - - - -
179B SER* 1.3 85.8 + - - +
181B VAL* 1.3 66.2 + - - +
182B TRP* 3.3 14.4 - - + -
392B VAL* 3.2 40.4 + - + +
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Residues in contact with VAL 181 (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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170B GLU* 4.0 34.8 - - + +
173B PHE* 4.1 22.7 - - + -
174B ARG* 4.2 30.1 + - + +
178B LEU* 4.2 16.2 - - + +
180B LYS* 1.3 80.3 - - - +
182B TRP* 1.3 69.8 + - - +
389B ILE* 5.0 0.7 - - + -
390B PHE 3.4 13.7 - - - +
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Residues in contact with TRP 182 (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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170B GLU* 5.3 1.8 - - - -
180B LYS* 3.3 17.3 - - + -
181B VAL* 1.3 86.1 - - - +
183B ARG* 1.3 68.4 + - - +
184B ASP* 5.3 2.2 - - + -
389B ILE* 3.8 2.1 - - - +
390B PHE* 2.8 70.3 + + + +
391B GLY 4.5 0.2 - - - -
392B VAL* 3.2 44.9 - - + -
449B ILE* 4.2 21.5 - - + -
466B TRP* 5.2 6.9 - + - +
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Residues in contact with ARG 183 (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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170B GLU* 3.4 26.0 - - - +
182B TRP* 1.3 81.1 - - - +
184B ASP* 1.3 64.9 + - - +
387B LEU* 5.3 7.4 - - + -
388B ASN 3.4 7.9 - - - +
389B ILE* 4.3 11.2 - - + +
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Residues in contact with ASP 184 (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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182B TRP* 5.3 2.9 - - + -
183B ARG* 1.3 79.3 - - - +
185B GLN* 1.3 62.1 + - - +
186B HIS* 2.8 29.3 + - - -
316B PHE* 3.5 14.5 - - - -
386B ILE 3.7 0.7 - - - +
387B LEU* 3.4 3.6 - - - -
388B ASN* 2.7 46.4 + - + +
390B PHE* 3.9 14.6 - - + -
466B TRP* 4.3 7.2 - - + -
470B TYR* 3.1 31.1 + - - -
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Residues in contact with GLN 185 (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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184B ASP* 1.3 76.1 + - - +
186B HIS* 1.3 63.6 + - - +
187B PHE* 4.5 19.6 - - + -
316B PHE* 2.9 25.9 - - + -
385B LYS* 3.7 31.7 + - + +
386B ILE 3.1 8.3 - - - +
387B LEU* 4.7 7.4 - - + +
903B NAG 5.5 7.9 - - - +
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Residues in contact with HIS 186 (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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184B ASP* 2.8 28.8 + - - -
185B GLN* 1.3 75.1 - - - +
187B PHE* 1.3 67.9 - - - +
188B VAL* 3.9 12.3 - - + -
315B SER 3.0 24.7 + - - +
316B PHE* 3.0 29.1 - + - -
385B LYS* 3.6 5.9 - - - +
386B ILE* 2.7 41.3 + - + +
388B ASN* 3.7 21.4 + - - -
462B GLY* 5.9 0.4 - - - -
465B GLU* 3.4 38.5 - - + +
466B TRP* 4.2 4.2 + - - -
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Residues in contact with PHE 187 (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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185B GLN* 4.5 20.0 - - + -
186B HIS* 1.3 79.3 - - - +
188B VAL* 1.3 62.0 + - - +
189B LYS 4.3 0.2 + - - -
307B ASP* 5.3 0.2 - - - +
310B THR* 5.7 0.5 - - - +
315B SER* 3.5 10.9 + - - -
316B PHE* 5.9 0.4 - - - -
317B ASN* 2.9 29.2 - - - -
321B PHE* 3.4 37.2 - + + -
383B GLU* 5.8 7.6 - - + +
384B ILE 3.5 7.2 - - - +
385B LYS* 3.7 44.6 - - + -
903B NAG 4.2 32.5 - - + +
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Residues in contact with VAL 188 (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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186B HIS* 3.9 7.8 - - + -
187B PHE* 1.3 73.7 - - - +
189B LYS* 1.3 60.8 + - - +
190B ILE* 4.5 10.8 - - + -
222B TYR* 6.1 0.2 - - - +
307B ASP* 3.6 31.0 - - + +
315B SER* 3.6 17.0 - - - +
383B GLU* 4.5 1.8 - - - -
384B ILE* 3.0 32.4 + - + +
386B ILE* 3.4 29.2 - - + -
455B ALA* 4.8 1.8 - - + -
461B VAL* 3.8 19.5 - - + -
465B GLU* 4.2 7.2 - - + -
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Residues in contact with LYS 189 (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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187B PHE 4.3 0.4 + - - -
188B VAL* 1.3 74.3 - - - +
190B ILE* 1.3 63.6 + - - +
222B TYR* 3.6 5.9 + - - -
307B ASP* 3.1 18.9 + - - +
309B TYR* 3.4 36.8 - - + -
381B LEU* 5.1 4.3 - - + -
382B LYS 3.8 7.4 - - - +
383B GLU* 4.2 13.2 - - + +
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Residues in contact with ILE 190 (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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156B GLU* 5.5 2.2 - - + -
157B ALA* 4.2 11.0 - - + +
188B VAL* 3.8 11.2 + - + -
189B LYS* 1.3 76.3 - - - +
191B GLN* 1.3 66.1 + - - +
192B VAL* 4.1 16.8 - - + -
222B TYR* 3.5 22.6 - - - +
309B TYR* 4.8 1.4 + - - -
381B LEU* 3.2 10.4 - - - +
382B LYS* 3.1 36.4 + - + +
384B ILE* 4.2 31.9 - - + -
455B ALA* 5.2 3.8 - - + -
458B PHE* 3.5 42.0 - - + -
461B VAL* 6.2 0.4 - - + -
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Residues in contact with GLN 191 (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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190B ILE* 1.3 83.2 - - - +
192B VAL* 1.3 65.2 + - - +
219B TYR* 3.3 19.2 + - + -
220B VAL 3.3 7.3 - - - +
221B ALA* 3.2 4.9 - - + +
222B TYR* 2.6 41.8 + - + +
223B SER* 2.7 33.6 + - - +
225B ALA* 4.9 0.2 - - - +
309B TYR* 5.5 5.4 + - - +
379B ASN* 3.7 33.7 + - + +
380B VAL 3.4 20.2 - - - +
381B LEU* 4.2 3.1 - - + +
382B LYS 4.5 0.4 - - - +
458B PHE* 4.0 10.5 - - - -
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Residues in contact with VAL 192 (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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156B GLU* 5.2 10.3 - - + -
190B ILE* 4.1 19.1 - - + -
191B GLN* 1.3 75.9 - - - +
193B LYS* 1.3 68.2 + - - +
219B TYR* 3.4 23.3 - - + +
379B ASN* 3.5 9.3 - - - +
380B VAL* 3.1 35.0 + - + +
382B LYS* 4.0 21.8 - - + -
458B PHE* 5.4 0.4 - - + -
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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
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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