Contacts of the strand formed by residues 155 - 160 (chain A) in PDB entry 1KWZ
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 ALA 155 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A ILE* 5.6 0.7 - - + -
151A ALA* 3.9 15.3 - - + -
153A THR 3.3 0.2 + - - -
154A SER* 1.3 75.6 - - - +
156A PHE* 1.3 61.7 + - - +
197A THR* 3.1 7.7 - - - -
198A ILE* 2.9 41.2 + - + +
213A HIS* 4.2 0.7 - - - -
214A THR* 3.2 22.9 - - - +
216A VAL* 3.6 23.3 - - + -
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Residues in contact with PHE 156 (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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119A MET 3.3 14.1 - - - -
121A PHE* 3.3 50.5 - + + -
124A VAL* 4.0 11.7 - - + -
135A VAL* 3.6 13.8 - - + +
136A ALA* 4.3 1.9 + - - +
155A ALA* 1.3 80.1 - - - +
157A LEU* 1.3 64.7 + - - +
195A CYS* 3.7 24.7 - - + -
196A VAL 3.5 13.5 - - - -
197A THR* 3.8 4.7 - - + -
207A ILE* 3.7 15.5 - - + -
208A SER 3.9 8.3 - - - -
209A CYS 4.0 1.6 - - - -
211A ALA 3.2 27.6 - - - -
213A HIS* 3.7 25.1 - + + +
214A THR 3.3 9.2 + - - +
216A VAL* 4.7 8.8 + - - +
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Residues in contact with LEU 157 (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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121A PHE* 3.4 15.9 - - - -
135A VAL* 3.4 5.8 - - - -
136A ALA 3.1 13.7 - - - +
138A PRO* 3.9 20.2 - - + -
147A ILE* 4.3 10.3 - - + -
156A PHE* 1.3 79.7 - - - +
158A GLY* 1.3 58.5 + - - +
159A ILE* 2.8 26.7 + - + +
196A VAL* 3.0 34.1 + - + +
198A ILE* 3.8 31.0 - - + +
204A TRP* 3.6 39.7 - - + +
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Residues in contact with GLY 158 (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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135A VAL* 3.4 13.1 - - - +
136A ALA 2.8 14.1 + - - -
137A ILE* 3.5 19.3 - - - +
157A LEU* 1.3 68.4 - - - +
159A ILE* 1.3 64.5 + - - +
170A TYR* 3.4 4.0 - - - -
171A VAL* 3.0 45.6 + - - -
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Residues in contact with ILE 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ILE* 4.6 1.3 - - + -
138A PRO* 4.1 18.4 - - + -
157A LEU* 2.8 19.8 + - + +
158A GLY* 1.3 82.1 - - - +
160A THR* 1.3 70.8 + - - +
168A PHE* 3.8 29.8 - - + -
169A MET 3.4 9.4 - - - +
170A TYR* 4.0 17.7 - - + -
171A VAL* 4.1 1.0 - - - +
176A LEU* 3.9 18.4 - - + -
181A TRP* 5.5 0.2 - - + -
195A CYS* 5.1 0.2 - - - -
196A VAL* 3.6 31.6 + - + +
204A TRP* 3.7 34.1 - - + -
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Residues in contact with THR 160 (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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121A PHE* 3.6 34.3 - - + -
159A ILE* 1.3 82.5 - - - +
161A ASP* 1.3 56.1 + - - +
162A GLU* 3.1 29.5 + - - +
163A VAL* 5.0 1.9 + - - +
167A GLN 4.1 0.2 - - - +
168A PHE* 3.5 8.3 - - - -
169A MET* 2.7 38.1 + - - +
171A VAL* 4.4 7.6 - - + +
194A ASP 3.0 19.1 - - - +
195A CYS* 3.9 7.6 - - - -
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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