Contacts of the strand formed by residues 168 - 173 (chain B) in PDB entry 1DY7
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
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Residue Dist Surf HB Arom Phob DC
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163B TRP* 4.1 30.1 - - + -
164B ASP 3.3 7.6 + - - +
165B LEU* 3.0 22.9 + - + +
167B ASN* 1.3 79.4 - - - +
169B PHE* 1.3 66.0 + - - +
170B SER* 6.3 0.2 - - - -
181B LEU* 4.1 19.7 - - + -
182B ILE 3.5 26.7 - - - +
183B ASP* 4.1 7.0 - - + +
184B GLY 4.5 1.1 - - - +
190B LYS* 4.2 5.6 - - + -
225B LEU* 4.1 25.8 - - + -
558B ASN* 3.3 3.6 - - - -
559B VAL* 2.9 38.3 + - + +
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Residues in contact with PHE 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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167B ASN 3.5 13.5 - - - -
168B LEU* 1.3 77.8 - - - +
170B SER* 1.3 58.4 + - - +
171B VAL* 3.9 7.4 - - + -
180B ALA 3.4 3.3 - - - +
181B LEU* 3.4 3.3 - - - -
182B ILE* 2.8 37.1 + - + +
184B GLY* 3.9 7.9 - - - -
509B GLU* 3.7 32.1 - - + -
510B PHE 3.5 17.7 - - - -
511B ASN* 3.6 13.7 - - + -
518B TRP* 3.5 70.4 - + + -
556B LYS* 4.4 8.5 - - + -
557B PHE 3.3 3.4 - - - -
558B ASN* 3.7 18.4 - - + -
559B VAL* 5.7 0.2 - - - -
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Residues in contact with SER 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B LEU* 6.3 0.2 - - - -
169B PHE* 1.3 71.4 - - - +
171B VAL* 1.3 60.1 + - - +
179B ILE* 3.8 13.3 - - - +
180B ALA 3.6 3.4 - - - -
181B LEU* 4.1 10.1 - - - -
202B SER* 2.8 32.0 + - - -
204B LEU* 5.7 1.8 - - - -
211B LEU* 3.7 23.6 - - - +
555B GLY 3.7 1.6 - - - +
556B LYS* 3.4 2.1 - - - -
557B PHE* 2.8 43.6 + - - -
559B VAL* 5.6 2.9 - - - +
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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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169B PHE* 4.3 11.0 - - + -
170B SER* 1.3 77.4 + - - +
172B THR* 1.3 73.1 + - - +
173B LEU* 3.5 6.8 + - + +
179B ILE* 3.1 6.8 - - - -
180B ALA* 2.7 43.6 + - + +
182B ILE* 3.8 28.0 - - + -
202B SER* 5.7 0.2 - - - -
518B TRP* 4.7 0.7 - - + -
531B LEU* 4.1 23.3 - - + -
550B LEU* 4.9 0.9 - - + -
553B PRO* 4.3 7.9 - - + -
554B THR 4.9 0.2 - - - +
555B GLY 3.3 8.3 - - - +
556B LYS* 4.0 24.9 - - + -
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Residues in contact with THR 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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170B SER 4.2 0.8 + - - -
171B VAL* 1.3 71.9 - - - +
173B LEU* 1.3 62.8 + - - +
174B ARG* 3.5 17.4 + - + +
178B GLN 4.0 4.0 - - - +
179B ILE* 4.3 4.1 - - - +
199B VAL* 3.2 50.3 + - + +
200B HIS 4.6 4.7 + - - -
201B ILE* 5.0 1.6 + - - -
202B SER* 5.0 4.0 + - - -
553B PRO* 3.2 6.6 - - - +
554B THR* 3.1 42.7 + - - +
555B GLY* 2.8 20.6 + - - -
557B PHE* 5.1 0.9 - - - -
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Residues in contact with LEU 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* 4.1 13.2 - - + +
172B THR* 1.3 78.1 - - - +
174B ARG* 1.3 67.3 + - - +
175B ASP 3.6 0.4 - - - -
176B ALA* 3.4 8.8 + - + -
177B GLY 3.3 11.1 + - - -
178B GLN* 2.9 32.7 + - + +
179B ILE 4.4 0.4 - - - -
180B ALA* 4.2 15.9 - - + +
192B VAL* 3.9 28.9 - - + -
199B VAL 5.7 0.2 + - - -
549B ARG 3.4 22.7 - - - +
550B LEU* 3.7 32.3 - - + -
551B VAL 3.1 22.0 - - - +
553B PRO* 4.5 2.2 - - + -
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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