Contacts of the strand formed by residues 196 - 200 (chain D) in PDB entry 3QUM
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 CYS 196 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140D GLY 4.8 0.4 - - - -
141D CYS* 2.0 53.6 - - - -
153D LEU* 6.2 2.0 - - + -
154D LEU 3.5 4.0 - - - -
155D TRP* 3.0 31.9 - - - -
195D THR* 1.3 83.8 + - - +
197D ASN* 1.3 62.9 + - - +
198D VAL* 3.6 6.9 + - + -
207D VAL* 3.2 1.9 - - - +
208D ASP* 3.1 26.9 - - - -
209D LYS* 3.4 12.1 + - + +
211D ILE* 5.5 3.4 - - - -
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Residues in contact with ASN 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D THR* 4.1 2.1 + - - -
153D LEU* 3.0 5.7 + - - -
154D LEU* 2.7 79.0 + - + +
156D ASN 4.1 0.4 - - - +
157D SER* 3.0 42.0 + - - +
195D THR 4.2 0.8 + - - +
196D CYS* 1.3 71.2 - - - +
198D VAL* 1.3 63.9 + - - +
207D VAL 3.3 8.7 - - - +
208D ASP* 3.1 19.2 - - - +
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Residues in contact with VAL 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D PRO* 6.0 3.1 - - + +
122D VAL* 3.8 35.7 - - + -
141D CYS* 4.5 14.1 - - + -
143D VAL* 5.0 13.9 - - + -
151D VAL* 4.5 9.6 - - + -
152D THR* 3.6 15.7 - - - +
153D LEU* 4.8 6.5 - - + -
196D CYS* 3.6 3.1 + - + +
197D ASN* 1.3 79.2 - - - +
199D ALA* 1.3 81.4 + - - +
200D HIS* 4.4 7.2 - - + +
205D THR* 5.0 2.0 - - + +
206D LYS* 3.6 2.8 - - - +
207D VAL* 3.2 36.9 + - + +
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Residues in contact with ALA 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D THR* 3.5 30.6 + - + +
198D VAL* 1.3 89.4 - - - +
200D HIS* 1.3 58.9 + - - +
201D PRO* 2.8 21.1 - - - +
205D THR 3.1 11.4 - - - -
206D LYS* 3.2 23.3 - - + +
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Residues in contact with HIS 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D THR 3.9 3.1 - - - -
119D ALA* 3.3 34.7 - - + +
120D PRO* 4.4 8.3 - - + -
146D TYR* 3.6 11.8 - - + +
148D PRO* 2.9 57.8 + - + +
150D SER 3.4 21.5 - - - -
151D VAL* 4.2 14.4 - - + -
198D VAL* 4.4 5.0 - - + +
199D ALA* 1.3 71.8 - - - +
201D PRO* 1.3 62.5 - - + +
202D ALA 4.0 3.7 + - - -
203D SER* 3.5 15.3 - - - -
204D SER 3.1 8.0 + - - -
205D THR* 3.0 25.6 + - - +
206D LYS* 3.8 0.9 - - - -
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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