Contacts of the strand formed by residues 200 - 205 (chain B) in PDB entry 3DGG
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 THR 200 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B TRP* 3.4 6.9 - - - -
161B ASN* 3.0 49.8 + - - +
198B THR* 4.4 12.1 - - - +
199B VAL* 1.3 80.3 - - - +
201B CYS* 1.3 64.1 + - - +
202B ASN* 3.4 13.7 + - - +
213B ASP* 4.1 12.5 - - - +
214B LYS 3.3 13.2 + - - -
215B LYS* 3.9 11.0 - - + -
216B ILE* 4.5 0.9 - - - +
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Residues in contact with CYS 201 (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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127B VAL* 4.1 10.5 - - - +
128B TYR 5.2 0.9 - - - -
129B PRO* 5.5 0.2 - - - -
146B CYS* 2.0 54.1 - - + -
158B VAL* 4.5 4.3 - - + -
159B THR 3.3 8.3 - - - +
160B TRP* 3.7 20.9 - - + -
200B THR* 1.3 72.1 - - - +
202B ASN* 1.3 60.4 + - - +
203B VAL* 4.1 1.0 + - + +
212B VAL 3.7 1.7 - - - +
213B ASP* 3.5 3.5 - - - -
214B LYS* 3.1 41.6 + - - +
216B ILE* 4.6 4.7 - - - -
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Residues in contact with ASN 202 (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 THR 3.4 2.1 - - - +
158B VAL* 3.2 4.9 - - - -
159B THR* 2.7 72.0 + - + +
161B ASN* 3.4 1.1 + - - +
162B SER* 3.3 27.4 + - - +
200B THR* 3.4 16.1 + - - +
201B CYS* 1.3 74.1 - - - +
203B VAL* 1.3 59.9 + - - +
213B ASP* 2.9 30.8 - - - +
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Residues in contact with VAL 203 (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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125B PRO* 4.4 6.3 - - + -
127B VAL* 3.9 22.2 - - + -
146B CYS* 4.3 9.0 - - - -
148B VAL* 3.8 33.7 - - + -
156B VAL* 3.3 28.7 - - + -
157B THR 3.3 3.1 - - - +
158B VAL* 4.0 10.1 - - + -
201B CYS* 4.7 0.2 - - - -
202B ASN* 1.3 79.7 - - - +
204B ALA* 1.3 62.3 + - - +
205B HIS 4.3 0.2 + - - -
210B THR* 3.6 1.7 - - - +
211B LYS* 3.5 3.5 - - - -
212B VAL* 2.9 45.2 + - + +
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Residues in contact with ALA 204 (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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156B VAL* 3.2 8.3 - - - +
157B THR* 2.8 49.6 + - + +
202B ASN 4.2 0.2 - - - -
203B VAL* 1.3 73.6 - - - +
205B HIS* 1.3 60.3 + - - +
206B PRO* 3.6 9.3 - - + +
210B THR 3.2 7.9 - - - +
211B LYS* 4.6 14.6 - - + +
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Residues in contact with HIS 205 (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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122B THR* 4.5 0.4 - - + -
123B THR 3.4 22.4 - - - -
125B PRO* 3.7 25.9 - - + +
151B TYR* 3.9 14.5 - + + -
152B PHE 3.4 12.9 + - - -
153B PRO 2.8 24.7 + - - -
155B PRO 3.3 20.4 - - - -
156B VAL* 4.3 2.9 - - + -
203B VAL 4.2 0.4 - - - -
204B ALA* 1.3 72.6 - - - +
206B PRO* 1.3 69.3 - - - +
207B ALA* 3.9 18.2 - - + +
208B SER* 2.6 30.1 + - - +
209B SER 3.1 4.0 + - - -
210B THR* 2.9 32.2 + - - -
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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