Contacts of the strand formed by residues 204 - 210 (chain D) in PDB entry 1CT8
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 204 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118D PRO* 3.6 12.9 - - + +
119D PRO* 4.5 14.6 - - + +
197D VAL 4.4 1.1 - - - +
198D ALA* 3.4 0.9 - - - +
199D HIS* 2.9 38.7 + - + +
202D SER* 2.5 32.3 + - - -
203D SER* 1.3 76.4 - - - +
205D LYS* 1.3 71.3 + - - +
206D VAL* 3.7 23.3 - - + -
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Residues in contact with LYS 205 (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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197D VAL 3.4 5.4 - - - -
198D ALA* 4.4 15.0 - - + +
203D SER 4.0 5.2 + - - +
204D THR* 1.3 80.9 - - - +
206D VAL* 1.3 63.2 + - - +
207D ASP* 4.4 1.7 + - - +
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Residues in contact with VAL 206 (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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119D PRO* 5.3 3.6 - - + +
121D VAL* 4.1 31.4 - - + -
195D CYS 3.7 1.3 - - - +
196D ASN* 3.4 0.7 - - - -
197D VAL* 2.8 39.6 + - + +
204D THR* 3.7 21.8 - - + -
205D LYS* 1.3 76.4 - - - +
207D ASP* 1.3 77.5 + - - +
208D LYS* 4.0 24.5 - - + +
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Residues in contact with ASP 207 (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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156D SER* 5.6 0.7 + - - -
194D THR* 3.9 10.5 - - + +
195D CYS 3.5 2.7 - - - -
196D ASN* 3.2 28.2 + - - +
205D LYS* 4.4 2.0 + - - +
206D VAL* 1.3 88.7 + - - +
208D LYS* 1.3 66.8 + - - +
209D LYS 3.9 1.9 + - - -
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Residues in contact with LYS 208 (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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123C GLU* 3.1 36.6 + - - +
121D VAL* 3.6 41.2 + - + +
123D PRO* 4.0 17.9 - - + -
140D CYS* 4.3 9.2 - - - -
194D THR* 3.5 3.4 - - - +
195D CYS 2.8 33.3 + - - +
206D VAL* 4.0 17.2 - - + +
207D ASP* 1.3 74.0 + - - +
209D LYS* 1.3 70.2 + - - +
210D ILE* 3.6 7.6 + - - +
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Residues in contact with LYS 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D PRO* 3.8 13.3 - - - +
192D THR* 3.5 36.1 - - + +
193D VAL 3.5 4.9 - - - +
194D THR* 3.3 23.5 + - - +
207D ASP 3.9 2.0 + - - -
208D LYS* 1.3 78.4 - - - +
210D ILE* 1.3 71.1 + - - +
211D VAL* 3.7 19.8 + - + +
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Residues in contact with ILE 210 (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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123D PRO* 3.7 20.2 - - + -
124D LEU 3.7 18.4 - - - +
125D ALA* 3.9 15.5 - - + -
138D LEU* 3.9 19.7 - - + -
139D GLY 3.5 22.9 - - - +
140D CYS* 4.2 3.8 - - - -
154D TRP* 3.9 21.8 - - + -
188D TRP* 3.1 27.4 + - + +
191D GLU 5.5 0.3 - - - +
192D THR* 5.6 0.7 - - - -
193D VAL* 2.7 29.3 + - + +
208D LYS 3.7 13.2 - - - +
209D LYS* 1.3 76.1 - - - +
211D VAL* 1.3 64.2 + - - +
212D PRO* 4.5 0.5 - - - +
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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