Contacts of the strand formed by residues 139 - 144 (chain A) in PDB entry 6WNX
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 139 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A TYR* 3.2 3.1 - - - +
136A ASP* 2.7 66.2 + - - +
138A GLU* 1.3 82.8 + - + +
140A ILE* 1.3 63.5 + - - +
141A ILE* 3.8 23.6 - - + -
151A ILE* 4.2 16.8 - - + -
152A TRP 3.3 13.7 - - - +
153A ASP* 5.2 0.2 - - - -
154A LYS* 3.6 4.1 - - - +
160A LEU* 5.2 4.0 - - + -
175A TYR* 3.7 21.3 - - - +
176A ASP 5.7 0.2 + - - -
194A VAL* 4.2 18.3 - - - +
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Residues in contact with ILE 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A ILE* 4.2 23.3 - - + -
133A LEU* 4.6 9.4 - - + -
134A GLN 3.5 10.3 - - - +
135A TYR* 3.8 17.7 - - + -
139A LYS* 1.3 74.8 - - - +
141A ILE* 1.3 69.0 + - - +
151A ILE* 3.4 2.1 - - - +
152A TRP* 2.7 46.8 + - + +
153A ASP 5.0 1.3 - - - +
154A LYS* 3.9 21.1 - - + -
157A LEU* 5.0 1.6 - - + -
393A ILE* 4.0 26.7 - - + -
401A ILE* 4.4 20.0 - - + -
403A ILE* 4.5 10.3 - - + -
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Residues in contact with ILE 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A LEU* 3.2 4.5 - - - +
134A GLN 2.8 33.2 + - - +
139A LYS* 3.8 26.0 - - + -
140A ILE* 1.3 76.0 - - - +
142A SER* 1.3 62.6 - - - +
149A ILE* 3.6 25.4 - - + -
150A LYS 3.6 4.9 - - - +
151A ILE* 4.1 15.9 - - + +
173A LEU* 4.1 14.8 - - + +
175A TYR* 3.5 40.4 - - + -
180A ILE* 3.9 27.6 - - + -
194A VAL* 4.3 3.1 - - + -
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Residues in contact with SER 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A CYS* 5.3 0.3 - - - -
130A VAL* 4.0 8.1 - - - -
132A CYS 3.4 11.4 - - - -
133A LEU* 4.5 2.2 - - - -
140A ILE* 5.1 0.2 - - - -
141A ILE* 1.3 76.1 - - - +
143A GLY* 1.3 59.3 + - - +
144A LEU* 3.6 11.2 - - - +
149A ILE* 3.3 7.8 - - - +
150A LYS 2.9 42.3 + - - -
152A TRP* 3.1 15.1 + - - -
173A LEU* 3.6 6.3 - - - -
401A ILE* 3.8 24.0 - - - +
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Residues in contact with GLY 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A VAL* 3.4 5.7 - - - +
131A TYR 2.8 30.8 + - - -
132A CYS* 3.1 24.4 + - - -
142A SER* 1.3 72.7 - - - +
144A LEU* 1.3 57.8 + - - -
148A SER 3.9 2.2 - - - -
149A ILE* 4.7 0.2 - - - -
170A VAL* 3.5 24.9 - - - -
173A LEU* 3.5 3.6 - - - +
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Residues in contact with LEU 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A CYS* 3.8 26.0 - - + +
124A SER* 3.2 22.0 - - - +
129A GLY 3.5 9.9 - - - +
130A VAL* 4.1 8.5 - - + +
131A TYR* 4.5 1.8 - - - -
142A SER* 3.6 31.0 - - - +
143A GLY* 1.3 80.6 - - - +
145A ARG* 1.3 59.7 + - - +
146A ASP* 3.2 15.0 - - - +
147A ASN* 3.1 16.3 + - - -
148A SER* 3.1 17.2 + - - +
150A LYS* 3.9 26.2 - - + +
170A VAL* 3.1 19.6 + - - +
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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