Contacts of the strand formed by residues 198 - 202 (chain G) in PDB entry 5AYZ
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 VAL 198 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168G VAL* 3.3 13.2 - - + +
170G VAL* 4.4 0.4 - - + -
185G VAL* 4.5 10.8 - - + -
188G ALA* 3.5 47.1 - - + +
189G ARG* 4.2 12.6 - - + +
192G ALA 5.9 2.2 - - - +
196G LEU 4.9 3.6 - - - +
197G LYS* 1.3 78.4 - - - +
199G GLU* 1.3 60.7 + - - +
200G VAL* 3.9 21.1 - - + -
215G GLY 4.9 2.5 - - - +
216G ALA* 3.7 5.2 - - - -
217G ASP* 2.7 43.3 + - - +
218G LEU* 3.1 6.9 + - - +
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Residues in contact with GLU 199 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160G HIS* 3.3 26.3 - - - -
167G LEU* 3.5 22.0 - - + +
168G VAL 2.9 6.6 + - - +
169G MET* 3.3 15.5 - - + +
170G VAL* 2.9 26.2 + - - +
198G VAL* 1.3 74.5 - - - +
200G VAL* 1.3 66.9 + - - +
218G LEU* 3.3 32.0 - - + +
220G LEU* 3.4 30.9 - - + +
246G GLU* 2.7 27.9 - - - +
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Residues in contact with VAL 200 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169G MET* 5.8 0.2 - - - -
170G VAL* 3.5 21.1 - - + +
175G VAL* 5.4 2.9 - - + -
181G VAL* 4.7 6.1 - - + -
185G VAL* 3.6 29.6 - - + -
198G VAL* 3.9 14.8 - - + -
199G GLU* 1.3 81.8 - - - +
201G GLU* 1.3 66.6 + - - +
202G CYS* 3.7 7.2 - - - -
207G GLU* 5.9 0.4 - - + -
211G ALA* 3.7 23.6 - - + -
216G ALA* 3.9 10.1 - - + -
218G LEU 3.0 9.0 + - - +
219G VAL* 3.6 4.6 - - + -
220G LEU* 2.9 29.6 + - - -
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Residues in contact with GLU 201 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169G MET* 3.5 12.0 - - + +
170G VAL 2.9 17.2 + - - +
171G LYS* 3.4 32.5 + - + +
172G ASP* 3.7 32.3 + - + +
175G VAL* 5.2 2.9 - - - +
200G VAL* 1.3 77.3 - - - +
202G CYS* 1.3 61.3 + - - +
203G SER 4.5 0.2 + - - -
207G GLU* 3.9 9.2 - - - +
220G LEU* 3.6 21.3 - - + -
222G ASP* 4.0 17.9 - - + +
401G NCN 2.8 30.0 + - - +
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Residues in contact with CYS 202 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200G VAL* 3.7 24.7 - - - -
201G GLU* 1.3 80.2 - - - +
203G SER* 1.3 59.8 + - - +
204G SER 4.1 4.3 - - - +
207G GLU* 3.2 14.8 - - - +
208G ALA* 3.5 43.1 - - + +
211G ALA* 4.1 2.7 - - - -
219G VAL* 4.1 7.2 - - - -
220G LEU 2.8 12.6 + - - +
221G LEU* 4.4 4.0 - - + -
222G ASP* 2.9 27.4 + - - -
224G PHE* 3.4 6.6 - - - -
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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