Contacts of the strand formed by residues 162 - 166 (chain A) in PDB entry 3KTC
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 162 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A ASN* 3.6 21.6 + - + +
122A TYR* 3.2 5.1 - - + -
123A VAL 2.9 25.5 + - - -
161A VAL* 1.3 79.8 - - - +
163A PHE* 1.3 60.8 + - - +
194A ASP 5.3 1.2 + - - -
195A ASN 3.4 4.5 - - - +
226A PHE* 3.7 42.3 - - + -
340A EDO 2.8 49.0 + - - +
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Residues in contact with PHE 163 (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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108A MSE 4.8 0.7 - - - -
112A ALA* 4.1 4.7 - - + -
123A VAL* 3.4 30.5 - - + -
125A VAL* 4.0 11.4 - - + -
151A MSE 5.1 5.2 - - - -
154A LEU* 3.5 41.7 - - + -
155A ALA* 3.8 15.5 - - + -
158A ASN* 3.7 35.7 - - + -
161A VAL* 3.4 30.3 - - + -
162A LYS* 1.3 71.6 - - - +
164A ALA* 1.3 59.4 + - - +
165A ILE 3.8 0.4 + - - -
195A ASN* 2.9 16.9 + - - +
196A VAL* 3.5 14.0 - - + +
197A GLY 2.9 27.0 + - - +
226A PHE* 3.6 2.1 - - - -
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Residues in contact with ALA 164 (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 TYR* 3.9 30.5 - - + +
123A VAL 2.8 8.1 + - - -
124A LYS* 3.6 4.0 - - - +
125A VAL* 2.8 27.2 + - - -
162A LYS 4.1 0.8 - - - -
163A PHE* 1.3 70.3 - - - +
165A ILE* 1.3 62.4 + - - +
166A GLU 3.5 0.9 + - - -
197A GLY 3.6 6.3 - - - -
199A LEU* 4.0 19.3 - - + +
226A PHE* 3.9 19.5 - - + -
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Residues in contact with ILE 165 (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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125A VAL* 3.5 9.6 - - + +
127A PRO* 5.2 2.0 - - + -
151A MSE 3.6 33.7 - - + -
163A PHE 4.8 0.9 - - - +
164A ALA* 1.3 72.5 - - - +
166A GLU* 1.3 62.6 + - - +
167A TYR 3.4 5.6 + - - +
178A TRP* 3.8 60.8 - - + -
184A THR* 4.1 8.5 - - + +
188A ILE* 4.3 5.8 - - + -
196A VAL* 3.5 27.4 - - + -
197A GLY 2.8 17.2 + - - +
198A VAL* 3.4 9.2 - - - +
199A LEU 2.9 18.9 + - - -
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Residues in contact with GLU 166 (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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124A LYS* 3.2 28.4 + - + +
125A VAL 2.9 15.2 + - - +
126A TRP* 3.2 24.0 - - + +
127A PRO* 4.7 0.2 - - - +
164A ALA 3.5 1.0 + - - -
165A ILE* 1.3 72.1 - - - +
167A TYR* 1.3 71.2 + - - +
176A MSE 3.7 5.4 - - - +
199A LEU* 3.5 21.1 - - + +
201A ASP* 3.2 8.4 - - + +
204A HIS* 3.3 8.3 - - + +
229A ASP* 3.0 7.4 - - - +
334A FE 2.0 30.8 - - - -
337A UNL 2.5 30.4 + - - -
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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