Contacts of the strand formed by residues 152 - 159 (chain B) in PDB entry 3K5N
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 TRP 152 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B LEU* 4.2 13.2 + - - +
151B LYS* 1.3 85.2 - - - +
153B VAL* 1.3 61.2 + - - +
171B GLU 5.6 0.2 - - - +
172B GLY* 3.1 4.7 - - - -
173B CYS* 2.9 27.8 + - - +
217B PRO* 4.4 2.0 - - - -
219B VAL* 3.4 28.8 - - + +
221B ILE* 3.4 29.2 - - + -
340B THR* 4.2 7.0 - - + -
343B PHE* 3.4 39.5 - + + -
344B HIS* 3.6 37.0 - + - -
349B MET* 3.6 36.5 - - + +
350B PRO* 5.1 3.1 - - + -
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Residues in contact with VAL 153 (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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152B TRP* 1.3 74.1 - - - +
154B SER* 1.3 63.0 + - - +
155B ILE* 4.6 2.9 - - + +
170B LEU* 3.6 26.0 - - + -
171B GLU 3.6 7.2 - - - +
211B TRP* 3.0 39.7 - - + -
212B PHE* 4.4 14.4 - - + -
217B PRO* 3.9 12.8 - - + -
219B VAL 3.2 12.1 + - - +
220B ILE* 4.2 15.5 - - + -
221B ILE* 3.0 23.3 + - - +
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Residues in contact with SER 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B TRP* 5.1 0.2 - - - +
153B VAL* 1.3 73.8 - - - +
155B ILE* 1.3 61.8 + - - +
169B GLY 3.4 4.5 - - - +
170B LEU* 3.5 0.7 - - - -
171B GLU* 2.7 43.2 + - - -
221B ILE* 3.4 20.7 + - - +
222B GLY* 4.7 0.3 - - - -
336B CYS* 3.0 36.7 + - - -
339B VAL* 3.9 11.8 - - - +
340B THR* 3.6 11.2 - - - -
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Residues in contact with ILE 155 (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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153B VAL* 3.8 4.9 + - + -
154B SER* 1.3 77.4 + - - +
156B ASP* 1.3 75.3 + - - +
157B ILE* 4.6 3.1 - - + -
168B ILE* 4.4 11.2 - - + -
169B GLY 3.5 3.1 - - - +
170B LEU* 4.0 24.0 - - + -
208B LEU* 4.7 7.9 - - + -
212B PHE* 5.3 5.6 - - + -
220B ILE* 4.7 8.3 - - + -
221B ILE 3.3 10.8 + - - +
222B GLY* 4.3 5.4 - - - -
225B VAL* 3.7 28.7 - - + -
229B ASP* 3.5 14.6 - - + +
230B LEU* 5.2 9.0 - - + -
233B LEU* 4.4 22.4 - - + -
246B LEU* 5.7 2.5 - - + -
336B CYS* 4.4 0.4 - - - -
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Residues in contact with ASP 156 (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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155B ILE* 1.3 79.1 - - - +
157B ILE* 1.3 102.5 + - - +
158B GLU* 3.9 5.4 - - - +
168B ILE* 3.4 1.4 - - - +
169B GLY 2.8 30.3 + - - -
228B PHE* 5.5 0.3 - - - -
229B ASP* 4.0 11.8 - - - +
293B LEU* 5.1 3.8 - - - +
332B ASN* 3.3 20.2 - - - +
335B ASN* 3.3 29.6 + - + +
336B CYS* 3.7 13.9 - - - +
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Residues in contact with ILE 157 (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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155B ILE* 4.6 4.0 - - + -
156B ASP* 1.3 106.0 + - - +
158B GLU* 1.3 65.8 + - - +
159B THR* 5.0 4.9 - - - -
165B LEU* 3.9 17.3 - - + -
167B CYS 3.1 10.5 - - - +
168B ILE* 4.0 18.4 - - + -
228B PHE* 3.7 28.6 - - + -
229B ASP* 3.6 25.7 + - + +
232B MET* 3.9 25.1 - - + -
233B LEU* 4.0 21.3 - - + -
236B HIS* 6.2 0.2 - - - +
332B ASN* 5.0 0.4 - - - +
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Residues in contact with GLU 158 (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 ASP* 3.9 8.0 - - - +
157B ILE* 1.3 77.9 - - - +
159B THR* 1.3 59.9 + - - +
165B LEU* 3.7 4.4 - - - +
166B TYR* 2.7 39.9 + - + +
167B CYS* 2.8 34.6 + - - +
317B ILE* 4.0 20.5 - - + +
328B LEU* 4.5 11.2 - - + -
331B TYR* 3.3 30.5 + - + -
332B ASN* 4.2 13.7 - - + +
335B ASN* 3.7 12.3 + - - -
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Residues in contact with THR 159 (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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157B ILE* 5.0 6.5 - - - +
158B GLU* 1.3 79.7 + - - +
160B THR* 1.3 68.0 + - - +
163B GLY* 2.5 45.6 - - - -
164B GLU 3.1 7.9 - - - -
165B LEU* 4.6 2.2 - - - -
166B TYR* 4.0 13.3 - - - +
228B PHE* 3.5 34.3 - - + -
232B MET* 5.5 0.9 - - - -
317B ILE* 4.6 9.0 - - - +
318B ASP* 5.3 0.3 - - - +
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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