Contacts of the strand formed by residues 201 - 206 (chain J) in PDB entry 3KYM
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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160J TRP* 3.1 11.3 - - - -
161J ASN* 2.9 35.9 + - - +
199J THR* 3.8 15.3 - - - +
200J TYR* 1.3 74.7 - - - +
202J CYS* 1.3 59.2 + - - +
203J ASN* 3.3 19.4 + - - -
214J ASP* 4.5 5.2 - - - +
215J LYS 3.2 13.2 - - - -
216J THR* 3.4 30.1 - - + +
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Residues in contact with CYS 202 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127J VAL* 3.9 14.1 - - - -
146J CYS* 2.0 50.5 - - + -
158J VAL* 4.6 6.5 - - + -
159J SER 3.6 6.7 - - - +
160J TRP* 3.6 20.6 - - + -
201J THR* 1.3 74.2 - - - +
203J ASN* 1.3 62.2 + - - +
204J VAL* 4.2 6.1 - - - -
213J VAL 3.6 1.6 - - - +
214J ASP* 3.4 1.2 - - - -
215J LYS 2.7 34.4 + - - -
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Residues in contact with ASN 203 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157J THR 3.3 2.1 - - - +
158J VAL* 2.2 36.0 - - - +
159J SER* 2.8 28.1 + - - +
161J ASN 4.7 0.2 - - - -
162J SER* 2.8 37.8 + - - +
201J THR* 3.3 21.6 + - - -
202J CYS* 1.3 71.8 - - - +
204J VAL* 1.3 61.5 + - - +
205J ASP* 5.1 1.6 - - + +
213J VAL 3.5 4.9 - - - -
214J ASP* 3.2 22.7 + - - +
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Residues in contact with VAL 204 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125J PRO* 4.7 7.2 - - + -
127J VAL* 3.6 37.5 - - + -
148J VAL* 3.5 42.8 - - + -
156J VAL* 3.6 15.0 - - + -
157J THR 3.5 4.3 - - - +
158J VAL* 4.6 7.2 - - + -
202J CYS* 4.2 10.8 - - - -
203J ASN* 1.3 75.4 - - - +
205J ASP* 1.3 66.2 + - - +
211J THR 3.9 0.6 - - - +
212J LYS* 3.6 1.4 - - - -
213J VAL* 2.7 38.3 + - + +
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Residues in contact with ASP 205 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156J VAL* 3.4 4.2 - - - +
157J THR* 2.8 59.9 + - + +
203J ASN* 5.1 1.8 - - + +
204J VAL* 1.3 79.1 - - - +
206J HIS* 1.3 85.1 + - - +
207J LYS* 3.8 14.3 + - - +
211J THR 3.3 12.5 + - - +
212J LYS* 4.9 13.9 + - + +
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Residues in contact with HIS 206 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123J LYS 3.6 9.6 + - - -
125J PRO* 3.9 21.5 - - + -
151J TYR* 4.2 6.3 - + + -
152J PHE 3.0 23.4 + - - -
153J PRO* 2.6 36.8 - - - +
155J PRO 3.2 15.5 + - - -
156J VAL* 4.5 2.2 - - + -
205J ASP* 1.3 79.5 + - - +
207J LYS* 1.3 58.9 + - - +
208J PRO* 3.6 15.2 - - + +
209J SER* 3.0 37.6 + - - -
210J ASN 2.9 21.7 + - - -
211J THR* 3.1 19.0 + - - +
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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