Contacts of the strand formed by residues 201 - 205 (chain X) in PDB entry 1T6B
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 201 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17X GLN* 4.5 4.8 + - - -
35X VAL 3.6 3.5 - - - +
36X THR* 2.8 23.1 + - - -
37X SER 4.6 0.7 + - - +
194X VAL* 4.4 10.5 - - + -
195X ASP 3.5 11.2 - - - +
196X VAL* 4.6 12.5 - - + +
199X LYS 3.5 3.7 + - - -
200X ARG* 1.3 73.7 + - - +
202X PHE* 1.3 72.1 + - - +
203X LEU* 5.3 2.2 - - + +
239X VAL 3.8 21.3 + - - +
240X THR* 4.0 29.9 + - - +
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Residues in contact with PHE 202 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34X VAL* 3.7 24.7 - - + -
35X VAL 3.9 1.3 - - - -
36X THR* 3.5 11.2 - - - -
45X ILE* 3.7 36.6 - - + -
49X GLU* 3.7 36.6 - - + -
50X LEU* 4.6 0.9 - - + -
53X ILE* 6.3 0.7 - - + -
193X THR 3.5 0.9 - - - +
194X VAL* 3.2 6.4 - - - +
195X ASP* 2.6 55.0 + - + +
197X LYS* 4.0 15.5 - - + -
200X ARG* 3.5 33.2 - - + -
201X THR* 1.3 79.2 - - - +
203X LEU* 1.3 61.5 + - - +
204X SER* 3.9 7.8 + - - +
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Residues in contact with LEU 203 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34X VAL* 3.5 1.2 - - - -
35X VAL* 2.8 53.7 + - + +
183X ILE* 3.8 35.7 - - + -
187X LEU* 3.1 31.5 - - + +
192X TYR* 3.7 26.0 - - + -
193X THR 3.5 1.8 - - - -
194X VAL* 4.1 7.2 - - + -
201X THR* 5.3 3.1 - - + +
202X PHE* 1.3 76.1 - - - +
204X SER* 1.3 63.3 + - - +
236X PHE* 4.4 15.5 - - + -
239X VAL* 4.5 10.5 - - + -
240X THR* 5.7 1.6 - - - +
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Residues in contact with SER 204 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33X MET 2.8 19.2 + - - -
34X VAL* 4.0 6.6 - - - +
52X ASN* 5.0 3.8 - - - +
53X ILE* 3.4 18.2 - - - +
187X LEU* 4.4 2.2 - - - -
192X TYR* 3.1 7.3 - - - -
193X THR* 2.7 48.4 + - - +
195X ASP* 6.2 1.6 - - - -
202X PHE* 4.6 8.5 - - - +
203X LEU* 1.3 78.1 + - - +
205X PRO* 1.3 67.3 - - - +
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Residues in contact with PRO 205 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32X PRO 3.6 20.0 - - - +
33X MET* 3.5 31.0 - - + +
52X ASN 5.0 0.9 - - - +
53X ILE* 4.8 2.6 - - + +
187X LEU* 3.6 19.9 - - + -
190X GLU* 6.5 0.7 - - + -
191X GLY 3.6 8.7 - - - +
193X THR* 4.1 0.6 - - - +
204X SER* 1.3 91.3 - - - +
206X TRP* 1.3 64.2 + - - +
207X ILE* 3.7 16.5 + - + +
211X HIS* 3.5 16.3 - - - -
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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