Contacts of the strand formed by residues 135 - 139 (chain C) in PDB entry 1WYK
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 LYS 135 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C DIO 3.6 27.3 - - - +
130C LEU 3.7 0.2 - - - +
131C ALA* 3.3 3.8 - - - -
132C MET 2.7 34.7 + - - +
133C GLU 3.7 7.6 + - - +
134C GLY* 1.3 82.3 - - - +
136C VAL* 1.3 59.8 + - - +
137C MET* 3.8 27.7 + - + +
166C PHE* 4.4 22.0 - - + -
167C ALA 3.3 14.8 - - - +
168C GLN* 4.6 10.6 - - + +
169C LEU* 3.5 8.7 - - - +
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Residues in contact with VAL 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C PHE* 4.7 0.9 - - + -
129C ALA* 4.4 7.4 - - + -
130C LEU 3.2 15.3 - - - +
131C ALA* 4.8 0.2 - - - -
135C LYS* 1.3 72.7 - - - +
137C MET* 1.3 65.3 + - - +
146C ILE* 3.9 24.5 - - + -
151C LEU* 4.2 18.8 - - + -
154C LEU* 4.0 16.4 - - + -
156C PHE* 4.0 8.9 - - + -
166C PHE* 3.2 4.5 - - - +
167C ALA* 2.9 49.5 + - + +
169C LEU* 3.7 16.7 - - + +
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Residues in contact with MET 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C DIO 3.6 26.9 - - - +
128C HIS 4.5 0.2 - - - +
129C ALA* 3.1 5.8 - - - -
130C LEU* 2.9 47.2 + - + +
132C MET* 3.8 27.8 - - + +
135C LYS* 3.8 26.9 - - + +
136C VAL* 1.3 76.5 - - - +
138C LYS* 1.3 62.3 + - - +
164C MET* 3.4 31.2 - - + -
165C GLU 3.2 8.7 - - - +
166C PHE* 4.0 10.8 - - + -
216C GLY* 5.4 0.5 - - - +
229C ILE* 4.0 3.8 - - + -
247C TRP* 4.0 7.2 - - + -
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Residues in contact with LYS 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C VAL* 4.1 20.9 - - + -
128C HIS 3.9 2.9 - - - +
129C ALA* 3.9 13.5 - - + -
137C MET* 1.3 75.0 - - - +
139C PRO* 1.3 86.5 + - + +
140C LEU 4.1 0.6 + - - -
142C VAL* 2.6 31.9 + - - -
144C GLY 4.7 7.7 + - - +
146C ILE* 4.2 23.8 - - + -
156C PHE* 5.1 5.6 - - + -
164C MET* 3.1 10.8 - - - +
165C GLU* 2.8 72.2 + - + +
216C GLY* 5.4 0.4 - - - -
229C ILE* 6.4 0.7 - - - -
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Residues in contact with PRO 139 (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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128C HIS 3.3 17.0 - - - +
138C LYS* 1.3 101.7 + - + +
140C LEU* 1.3 66.0 + - - +
141C HIS* 3.7 26.9 - - + +
142C VAL* 3.2 17.0 + - + +
163C ASP 3.3 11.0 - - - +
164C MET* 4.0 2.9 - - + -
215C SER* 3.7 9.6 - - - +
216C GLY* 3.4 27.6 - - - +
229C ILE* 5.2 2.5 - - + -
230C VAL 4.4 4.0 - - - +
231C LEU* 4.3 6.7 - - + -
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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