Contacts of the strand formed by residues 181 - 190 (chain B) in PDB entry 4K71
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 SER 181 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179B PRO 3.9 1.8 + - - -
180B PRO* 1.3 73.5 - - - +
182B MET* 1.3 60.4 + - - +
183B ARG* 4.8 3.8 - - - -
200B ALA* 3.6 1.9 - - - -
201B PHE* 2.9 41.3 + - - -
202B SER* 5.8 1.4 - - - -
13C HIS* 5.5 2.8 + - - -
14C PRO* 3.7 29.6 - - - +
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Residues in contact with MET 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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180B PRO* 3.7 17.3 - - - +
181B SER* 1.3 75.7 - - - +
183B ARG* 1.3 90.5 + - - +
198B CYS* 3.6 28.7 - - - -
199B SER 3.2 24.0 - - - +
200B ALA* 3.7 20.0 - - + -
210B LEU* 3.8 15.7 - - + -
254B VAL* 3.7 29.6 - - + -
263B LEU* 4.0 17.4 - - + +
265B VAL* 3.6 23.2 - - + +
268B GLU* 4.6 2.3 - - - +
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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
----------------------------------------------------------
181B SER* 4.8 2.8 - - - -
182B MET* 1.3 105.5 + - - +
184B LEU* 1.3 60.7 + - - +
185B LYS* 4.2 0.9 - - + -
197B THR 3.6 1.3 - - - +
198B CYS* 3.5 4.5 - - - -
199B SER* 2.8 33.3 + - - +
201B PHE* 4.1 11.4 - - + -
265B VAL* 3.9 5.4 - - - -
268B GLU* 3.8 32.4 + - + -
14C PRO* 3.6 41.3 + - + +
15C ALA 5.5 4.0 + - - -
16C GLU* 5.8 1.6 + - - -
98C ASP* 3.9 30.9 + - + +
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Residues in contact with LEU 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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183B ARG* 1.3 74.4 - - - +
185B LYS* 1.3 61.1 + - - +
196B LEU* 4.4 14.6 - - + -
197B THR 3.5 21.8 - - - +
198B CYS* 3.9 12.8 - - + +
212B PHE* 4.1 14.6 - - + -
250B TYR 4.1 1.3 - - - +
251B CYS* 3.7 21.3 - - - +
252B CYS* 4.0 4.0 - - + +
265B VAL* 3.5 36.7 - - + +
266B GLU 3.8 4.0 - - - +
267B LEU* 3.3 30.3 - - + +
268B GLU* 3.1 33.0 + - - +
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Residues in contact with LYS 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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183B ARG* 5.5 0.9 - - + -
184B LEU* 1.3 76.5 - - - +
186B ALA* 1.3 66.8 + - - +
187B ARG* 4.0 33.4 - - - +
195B VAL 3.8 1.0 - - - +
196B LEU* 3.4 4.4 - - - -
197B THR* 2.9 32.3 + - - -
267B LEU* 5.4 2.5 - - - +
268B GLU* 5.1 8.1 - - + +
96C ASP* 5.4 2.6 + - - -
97C ARG* 3.3 47.2 + - - +
98C ASP* 4.1 20.6 + - + +
99C MET* 3.8 17.1 - - - +
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Residues in contact with ALA 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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185B LYS* 1.3 79.7 - - - +
187B ARG* 1.3 73.5 + - - +
188B PRO* 4.8 1.4 - - - +
194B SER* 4.8 1.1 - - - -
195B VAL 3.3 5.6 - - - +
196B LEU* 3.3 25.6 - - + -
247B GLU* 3.9 17.5 - - + -
267B LEU* 4.3 12.3 - - + +
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Residues in contact with ARG 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 LYS* 4.0 22.8 - - - +
186B ALA* 1.3 77.5 + - - +
188B PRO* 1.3 90.5 - - - +
194B SER* 3.2 8.9 - - - -
195B VAL* 2.9 34.2 + - + -
96C ASP* 4.9 14.8 - - - +
99C MET* 3.8 32.2 - - + +
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Residues in contact with PRO 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 ALA 4.8 0.9 - - - +
187B ARG* 1.3 114.9 - - + +
189B SER* 1.3 59.9 + - - +
193B PHE 3.9 7.2 - - - +
194B SER* 4.3 5.6 - - - +
195B VAL* 4.7 2.1 - - - +
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Residues in contact with SER 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 ARG 3.7 0.2 + - - -
188B PRO* 1.3 75.2 - - - +
190B SER* 1.3 69.8 + - - -
193B PHE* 2.9 33.9 + - - +
194B SER 3.5 3.8 + - - -
195B VAL* 3.7 26.9 - - - -
241B THR* 4.6 4.8 - - - +
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Residues in contact with SER 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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189B SER* 1.3 82.5 + - - +
191B PRO* 1.3 82.3 + - - +
192B GLY 3.1 0.3 + - - -
193B PHE* 2.8 42.1 + - - +
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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