Contacts of the strand formed by residues 159 - 163 (chain C) 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 SER 159 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148C TRP* 4.1 18.4 - - - +
155C GLN 6.1 0.2 - - - -
156C SER* 5.5 1.4 - - - -
157C GLY 3.3 9.2 + - - +
158C ASN* 1.3 84.7 + - - +
160C GLN* 1.3 68.8 + - - +
177C SER* 4.4 4.0 - - - -
178C THR 2.9 17.3 - - - -
179C LEU* 3.9 10.5 - - - -
180C THR* 4.7 1.8 - - - +
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Residues in contact with GLN 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C SER* 1.3 79.1 - - - +
161C GLU* 1.3 60.6 + - - +
162C SER* 4.2 1.4 + - - -
176C SER* 3.9 1.9 + - - +
177C SER* 3.8 2.0 - - - -
178C THR* 2.8 38.8 + - - +
180C THR* 5.6 3.1 + - - +
175D VAL* 3.4 26.4 - - + +
176D LEU 2.9 26.5 + - - -
177D GLN* 3.6 29.1 - - - +
178D SER 4.9 1.2 - - - +
183D SER* 5.8 0.5 - - - -
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Residues in contact with GLU 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C ALA 5.3 5.0 - - - +
146C VAL* 4.1 17.2 - - + +
159C SER 4.4 0.2 - - - -
160C GLN* 1.3 72.9 - - - +
162C SER* 1.3 65.2 + - - +
163C VAL* 4.8 7.8 - - + +
175C LEU* 4.4 20.2 - - + +
176C SER 3.1 9.9 - - - +
177C SER* 4.1 11.9 + - - +
175D VAL* 4.1 11.3 - - - +
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Residues in contact with SER 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C GLN 5.1 1.3 - - - -
161C GLU* 1.3 78.3 - - - +
163C VAL* 1.3 62.5 + - - +
175C LEU* 3.2 5.3 - - - +
176C SER* 2.7 48.4 + - - -
172D PHE* 3.3 26.5 - - - +
173D PRO* 3.4 17.2 + - - +
175D VAL* 3.8 17.9 - - - -
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Residues in contact with VAL 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C PHE* 5.6 0.9 - - + -
142C ARG* 3.3 42.0 - - + +
161C GLU* 4.8 10.1 - - + +
162C SER* 1.3 77.9 + - - +
164C THR* 1.3 76.3 + - - +
165C GLU* 4.1 6.9 - - - +
173C TYR* 4.5 12.8 - - + -
174C SER 3.5 10.8 - - - +
175C LEU* 3.9 25.1 - - + -
173D PRO* 3.2 20.6 - - - +
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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