Contacts of the strand formed by residues 203 - 208 (chain C) in PDB entry 4YHP
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 ILE 203 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C TRP* 3.4 7.0 - - - -
163C ASN* 2.8 47.1 + - - +
201C THR* 4.1 20.0 - - + -
202C TYR* 1.3 78.5 - - - +
204C CYS* 1.3 69.5 + - - +
205C ASN* 3.5 21.8 + - - +
216C ASP* 3.9 10.1 - - + -
217C LYS 3.3 16.6 - - - +
218C LYS* 4.0 16.6 - - + +
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Residues in contact with CYS 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C VAL* 3.8 7.6 - - - -
148C CYS* 2.0 50.0 - - + -
160C VAL* 4.4 6.7 - - + -
161C SER 3.5 5.4 - - - +
162C TRP* 3.5 23.6 - - + -
203C ILE* 1.3 73.7 - - - +
205C ASN* 1.3 60.1 + - - +
206C VAL* 4.0 7.2 - - - -
215C VAL 3.6 1.0 - - - +
216C ASP* 3.5 4.3 - - - -
217C LYS* 3.0 45.6 + - - -
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Residues in contact with ASN 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C THR 3.5 1.9 - - - +
160C VAL* 3.3 5.3 - - - -
161C SER* 2.7 52.8 + - - +
163C ASN* 3.4 3.0 + - - +
164C SER* 2.7 41.2 + - - +
203C ILE* 3.5 15.7 + - - +
204C CYS* 1.3 70.5 - - - +
206C VAL* 1.3 61.7 + - - +
207C ASN* 3.9 2.1 + - - +
216C ASP* 2.6 33.6 + - - +
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Residues in contact with VAL 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C PRO* 4.1 14.6 - - + -
129C VAL* 3.8 19.1 - - + -
150C VAL* 3.7 37.5 - - + -
158C VAL* 3.7 22.0 - - + -
159C THR 3.5 3.1 - - - +
160C VAL* 4.4 7.6 - - + -
204C CYS* 4.0 20.0 - - - -
205C ASN* 1.3 74.4 - - - +
207C ASN* 1.3 64.0 + - - +
208C HIS 4.3 0.2 - - - -
213C THR* 3.9 0.9 - - - +
214C LYS* 3.4 3.1 - - - +
215C VAL* 2.7 43.9 + - + +
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Residues in contact with ASN 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C VAL* 3.2 6.6 - - - +
159C THR* 3.0 52.8 + - - +
205C ASN 3.9 2.2 + - - +
206C VAL* 1.3 74.0 - - - +
208C HIS* 1.3 61.4 + - - +
209C LYS* 3.4 43.2 + - - +
213C THR 3.6 2.8 + - - +
214C LYS* 3.3 35.3 - - + +
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Residues in contact with HIS 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C LYS 3.3 24.5 + - - -
127C PRO* 3.6 27.6 - - + +
153C TYR* 4.0 12.8 - + + -
154C PHE 3.4 14.3 - - - -
155C PRO 2.8 23.4 + - - -
157C PRO 3.3 22.0 - - - -
158C VAL* 4.4 3.1 - - + -
206C VAL 4.3 0.2 - - - -
207C ASN* 1.3 73.8 - - - +
209C LYS* 1.3 62.9 + - - +
210C PRO* 3.7 8.4 - - + +
211C SER* 2.5 42.3 + - - +
212C ASN 3.2 8.7 + - - -
213C THR 2.7 20.7 + - - +
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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
------------------------------------------------------------
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