Contacts of the strand formed by residues 123 - 128 (chain A) in PDB entry 1K89
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 GLY 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A PHE* 3.1 25.5 + - - +
82A ASN 2.7 20.4 + - - +
88A TYR* 4.0 3.1 - - - +
89A LEU 3.5 5.6 - - - +
107A GLY 4.4 2.2 - - - -
110A GLN* 4.1 0.2 - - - -
111A ALA* 3.7 27.7 - - - +
114A ASP* 3.9 1.6 - - - -
122A GLY* 1.3 74.6 - - - -
124A ALA* 1.3 62.9 + - - +
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Residues in contact with ALA 124 (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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78A ARG* 3.8 25.1 - - - +
79A VAL 3.1 17.7 - - - +
80A GLN* 4.0 4.0 - - - -
81A PHE 4.3 0.9 - - - +
88A TYR* 3.8 19.5 - - + -
89A LEU 2.8 6.7 + - - +
90A GLY* 3.1 20.3 - - - -
107A GLY* 4.2 6.7 - - - -
110A GLN* 3.3 12.4 - - - +
123A GLY* 1.3 75.1 - - - +
125A LYS* 1.3 64.3 + - - +
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Residues in contact with LYS 125 (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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78A ARG* 3.4 10.8 - - - +
79A VAL* 2.9 31.6 + - + +
91A GLY 3.6 22.4 - - - +
93A ARG* 5.3 2.2 - - - -
103A MET* 3.6 33.8 - - + +
106A LEU* 3.5 35.6 + - + +
107A GLY* 3.7 6.7 - - - +
110A GLN* 3.5 20.5 + - - +
113A LYS* 6.0 0.8 - - - +
124A ALA* 1.3 81.6 - - - +
126A GLY* 1.3 61.0 + - - +
165A ASP* 2.9 37.6 + - - -
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Residues in contact with GLY 126 (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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77A TYR 3.1 15.9 - - - -
78A ARG* 3.3 9.0 - - - +
91A GLY 3.1 8.8 + - - +
92A LEU* 3.2 10.2 - - - -
93A ARG* 2.9 18.4 + - - +
103A MET* 3.3 19.7 - - - +
125A LYS* 1.3 77.0 - - - +
127A GLY* 1.3 58.0 + - - -
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Residues in contact with GLY 127 (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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76A GLY* 3.4 3.8 - - - -
77A TYR* 2.8 38.0 + - - -
92A LEU* 3.8 6.6 - - - +
93A ARG 3.0 17.0 - - - -
94A PHE* 4.2 8.1 - - - -
98A VAL* 4.6 1.1 - - - -
103A MET* 3.7 4.5 - - - -
126A GLY* 1.3 75.7 - - - -
128A SER* 1.3 59.9 + - - -
147A PHE* 3.5 7.5 - - - -
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Residues in contact with SER 128 (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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74A ASN* 3.7 2.8 - - - +
75A THR 2.7 23.5 + - - -
77A TYR* 4.5 0.2 - - - -
93A ARG 3.0 7.4 + - - +
94A PHE* 3.5 10.8 - - - -
95A ALA 3.1 25.1 + - - +
98A VAL* 3.7 11.7 - - - +
127A GLY* 1.3 73.8 - - - -
129A ASP* 1.3 61.7 + - - +
130A PHE* 3.0 16.4 + - - +
143A PHE* 3.4 29.1 - - - -
147A PHE* 4.2 4.9 - - - -
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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