Contacts of the strand formed by residues 168 - 173 (chain B) in PDB entry 1F14
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 LEU 168 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A THR* 4.6 3.6 - - + -
235A ALA* 3.5 34.3 - - + +
238A LEU* 3.9 24.2 + - + +
239A GLY* 3.6 15.5 - - - +
159B PHE* 4.5 2.9 - - - -
160B PHE* 3.7 30.8 + - + -
166B MET* 3.2 10.3 - - + +
167B LYS* 1.3 79.5 - - - +
169B VAL* 1.3 68.6 + - - +
170B GLU* 4.5 3.6 - - + -
194B LYS* 4.7 2.0 - - - +
195B HIS 3.2 18.6 - - - +
197B VAL* 3.9 26.2 - - + -
207B VAL* 3.7 17.3 - - + -
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Residues in contact with VAL 169 (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 LEU* 3.7 31.2 - - + -
158B HIS 3.3 15.0 - - - +
159B PHE* 4.0 22.9 - - + -
160B PHE* 4.7 0.4 - - - -
168B LEU* 1.3 82.2 - - - +
170B GLU* 1.3 66.9 + - - +
171B VAL 3.7 0.2 + - - -
189B SER* 3.5 29.2 - - - +
194B LYS* 3.9 12.1 - - + -
195B HIS 3.3 1.1 + - - +
196B PRO* 3.2 14.4 - - + +
197B VAL* 3.1 21.7 + - - +
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Residues in contact with GLU 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B GLY 3.6 2.3 - - - +
157B LEU* 3.6 1.4 - - - -
158B HIS* 2.7 67.7 + - + +
160B PHE* 3.3 20.7 - - + -
168B LEU* 4.5 4.0 - - + -
169B VAL* 1.3 72.2 - - - +
171B VAL* 1.3 61.0 + - - +
172B ILE* 3.6 13.4 + - + +
197B VAL* 3.5 22.2 - - + +
199B CYS* 5.5 1.8 - - + -
204B GLY 4.8 0.5 - - - +
205B PHE* 3.7 13.1 - - - +
206B ILE* 3.0 17.1 + - + +
207B VAL* 2.9 29.6 + - - +
208B ASN 5.4 0.2 + - - -
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Residues in contact with VAL 171 (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 ALA* 5.5 0.7 - - + -
156B GLY 3.4 7.6 - - - +
157B LEU* 4.0 9.9 - - + -
169B VAL 4.4 1.1 - - - +
170B GLU* 1.3 73.1 - - - +
172B ILE* 1.3 64.7 + - - +
173B LYS 3.7 1.4 + - - -
182B PHE* 3.7 35.0 - - + +
185B LEU* 3.9 29.4 - - + +
186B VAL* 4.6 5.6 - - + -
189B SER* 4.0 12.8 - - - +
196B PRO* 3.9 26.9 - - + -
197B VAL 2.9 11.6 + - - +
198B SER* 3.7 3.8 + - - -
199B CYS 3.5 19.8 + - - +
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Residues in contact with ILE 172 (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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141B ILE* 3.9 6.1 - - + +
155B ALA* 3.1 11.3 - - - +
156B GLY* 2.7 50.6 + - - +
158B HIS* 5.0 0.9 - - + -
170B GLU* 4.1 15.7 - - + +
171B VAL* 1.3 76.7 - - - +
173B LYS* 1.3 61.7 + - - +
174B THR 4.0 0.7 + - - -
199B CYS* 3.5 24.5 - - + +
200B LYS 3.7 3.1 - - - +
201B ASP* 3.6 36.3 - - + -
205B PHE* 3.3 50.7 - - + -
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Residues in contact with LYS 173 (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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171B VAL 3.7 1.4 + - - +
172B ILE* 1.3 74.7 - - - +
174B THR* 1.3 64.0 + - - +
175B PRO* 4.8 0.2 - - - +
177B THR* 3.3 42.0 - - + -
178B SER 3.7 8.5 - - - -
179B GLN* 2.7 41.0 + - - +
182B PHE* 3.8 31.3 - - + +
198B SER* 5.6 2.2 - - - +
199B CYS 3.5 6.3 + - - +
200B LYS* 4.0 8.8 - - - +
201B ASP 3.9 13.2 + - - -
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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