Contacts of the strand formed by residues 164 - 170 (chain B) in PDB entry 5F0P
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 ILE 164 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B SER* 1.3 71.7 - - - +
165B LYS* 1.3 61.9 + - - +
166B MSE 5.3 2.9 - - + -
178B PHE* 4.1 13.5 - - + -
179B GLU* 3.2 7.3 - - - +
180B TYR* 2.9 47.5 + - + +
182B LYS 3.7 18.2 - - - +
183B SER* 3.8 19.1 - - - +
290B GLN* 3.6 35.0 - - + +
291B GLU 3.8 23.3 - - - +
292B ILE* 4.1 11.0 - - + -
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Residues in contact with LYS 165 (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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163B SER* 3.8 10.1 + - - +
164B ILE* 1.3 77.8 - - - +
166B MSE 1.3 71.8 + - - +
177B GLU* 3.5 29.9 + - + +
178B PHE 3.5 11.2 - - - +
179B GLU* 3.6 34.5 + - + +
194B LYS* 5.3 3.8 - - - +
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Residues in contact with MSE 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B ILE* 5.3 2.7 - - + -
165B LYS* 1.3 84.7 - - - +
167B GLU* 1.3 59.7 + - - +
168B VAL* 3.8 13.7 - - + -
177B GLU* 3.3 9.1 - - - +
178B PHE* 3.1 60.0 + - + -
288B LYS* 4.2 10.8 - - - +
290B GLN* 3.5 26.5 - - - +
559D THR* 3.1 44.0 - - + +
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Residues in contact with GLU 167 (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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166B MSE 1.3 73.8 - - - +
168B VAL* 1.3 65.6 + - - +
176B ILE 3.4 15.3 - - - +
177B GLU* 4.3 7.4 + - + +
198B LEU* 3.4 18.8 - - + +
415B ZN 2.0 39.8 - - - -
559D THR* 3.7 7.2 - - - +
560D MSE 3.3 37.1 + - + +
563D HIS* 3.4 26.8 - - - +
565D HIS* 3.2 6.8 + - - -
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Residues in contact with VAL 168 (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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166B MSE 3.8 23.5 + - + -
167B GLU* 1.3 78.6 - - - +
169B GLY* 1.3 59.9 + - - +
175B HIS* 3.8 1.6 - - - -
176B ILE* 2.9 55.4 + - + +
178B PHE* 3.8 28.0 - - + -
276B LEU* 5.6 0.2 - - + -
288B LYS* 4.1 17.0 - - + -
557D MSE 4.0 20.6 - - + -
558D ASN 3.2 13.0 - - - +
559D THR* 4.5 0.4 - - - -
560D MSE 4.1 6.6 - - - +
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Residues in contact with GLY 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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168B VAL* 1.3 77.2 - - - +
170B ILE* 1.3 70.5 + - - +
174B LEU 3.1 12.6 - - - -
557D MSE 3.5 12.1 - - - +
558D ASN* 2.9 35.2 + - - +
560D MSE 3.7 15.7 - - - +
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Residues in contact with ILE 170 (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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169B GLY* 1.3 82.1 - - - +
171B GLU* 1.3 68.9 + - - +
172B ASP 3.2 0.2 + - - -
173B CYS* 2.9 36.9 + - + -
174B LEU* 2.8 21.5 + - + +
175B HIS* 4.2 1.7 - - - -
286B TYR* 3.9 31.2 - - + -
133C PRO* 4.0 22.0 - - + -
555D TYR* 4.5 7.9 - - + -
556D LEU 4.0 18.6 - - - +
557D MSE 4.4 9.0 - - + -
558D ASN* 5.0 7.9 - - - +
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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