Contacts of the strand formed by residues 202 - 207 (chain X) in PDB entry 3HI6
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 202 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161X TRP* 3.4 6.9 - - - -
162X ASN* 2.8 42.0 + - - -
200X THR* 3.9 7.6 + - - +
201X TYR* 1.3 76.7 + - - +
203X CYS* 1.3 61.0 + - - +
204X ASN* 3.7 20.7 - - - +
215X ASP* 3.8 11.0 - - + -
216X LYS 3.5 27.1 - - - +
217X ARG* 3.9 18.2 + - + +
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Residues in contact with CYS 203 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128X VAL* 4.1 0.7 - - - -
147X CYS* 2.0 50.9 - - + -
159X VAL* 4.3 7.0 - - + -
160X SER 3.3 6.7 - - - +
161X TRP* 3.7 25.7 - - + -
202X THR* 1.3 73.2 - - - +
204X ASN* 1.3 59.0 + - - +
205X VAL* 4.0 15.0 - - - -
214X VAL 3.6 1.7 - - - +
215X ASP* 3.5 2.9 - - - -
216X LYS* 3.0 36.4 + - - -
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Residues in contact with ASN 204 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158X THR* 3.6 2.1 + - - +
159X VAL* 3.5 4.4 - - - -
160X SER* 2.7 50.8 + - - +
162X ASN 3.7 1.6 + - - -
163X SER* 2.8 40.0 + - - +
202X THR* 3.7 18.1 + - - +
203X CYS* 1.3 70.9 - - - +
205X VAL* 1.3 63.7 + - - +
206X ASP* 3.9 1.1 + - - +
215X ASP* 2.7 35.7 + - - +
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Residues in contact with VAL 205 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126X PRO* 4.2 10.1 - - + -
128X VAL* 4.0 18.2 - - + -
149X VAL* 3.8 37.5 - - + -
157X VAL* 3.5 23.6 - - + -
158X THR 3.5 4.5 - - - +
159X VAL* 4.4 7.4 - - + -
203X CYS* 4.0 21.1 - - - -
204X ASN* 1.3 75.8 - - - +
206X ASP* 1.3 62.5 + - - +
212X THR 4.6 0.7 - - - +
213X LYS* 3.3 4.3 - - - +
214X VAL* 2.7 44.8 + - + +
215X ASP* 5.3 0.2 - - - +
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Residues in contact with ASP 206 (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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157X VAL* 3.1 7.1 - - - +
158X THR* 3.0 48.4 + - - +
204X ASN 5.2 1.6 - - - +
205X VAL* 1.3 76.6 - - - +
207X HIS* 1.3 62.0 + - - +
208X LYS* 3.2 46.3 + - - +
211X ASN 5.2 1.0 - - - -
212X THR 3.3 6.4 + - - +
213X LYS* 3.2 30.8 - - + +
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Residues in contact with HIS 207 (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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124X LYS 3.2 26.4 + - - -
125X GLY* 3.6 1.6 - - - -
126X PRO* 3.6 22.0 - - + -
152X TYR* 3.8 13.0 - + + -
153X PHE 3.2 15.7 - - - -
154X PRO 2.6 23.7 + - - -
156X PRO 3.2 22.0 - - - -
157X VAL* 3.8 5.4 - - + -
205X VAL* 4.3 0.6 - - - +
206X ASP* 1.3 73.2 + - - +
208X LYS* 1.3 64.6 + - - +
209X PRO* 3.3 17.6 - - + +
210X SER* 2.6 38.8 + - - +
212X THR 2.7 23.7 + - - +
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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