Contacts of the strand formed by residues 133 - 139 (chain A) in PDB entry 1KIX
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 GLN 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A ALA* 2.8 42.4 + - + +
95A SER* 5.8 1.8 - - - +
97A TYR* 3.2 43.4 + - - +
99A THR* 3.8 19.3 - - + +
129A LEU* 3.4 9.8 - - - -
130A TYR 2.9 31.1 + - - +
131A ASN* 4.1 11.3 - - - +
132A GLY* 1.3 81.6 - - - +
134A ARG* 1.3 69.5 + - - +
135A GLN* 3.2 2.4 + - + +
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Residues in contact with ARG 134 (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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41A LEU 3.8 16.7 + - - -
42A ALA* 3.6 33.7 + - - +
44A ALA 4.2 13.9 + - - -
46A LEU* 5.9 4.4 - - - +
83A LEU* 3.9 21.8 - - + +
97A TYR 5.0 1.2 + - - -
98A ALA* 3.2 18.0 - - + +
99A THR* 3.0 24.3 + - - +
127A LEU* 3.7 24.4 - - + +
128A ARG 3.9 1.6 - - - -
129A LEU* 4.4 13.9 - - + +
133A GLN* 1.3 72.0 - - - +
135A GLN* 1.3 59.8 + - - +
136A PHE* 4.0 1.8 - - + -
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Residues in contact with GLN 135 (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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99A THR* 3.2 21.1 + - - +
101A VAL* 4.1 13.5 - - + +
127A LEU* 3.5 3.6 - - - +
128A ARG* 2.8 39.4 + - - +
130A TYR* 3.2 31.4 - - + +
133A GLN* 3.2 2.2 + - + +
134A ARG* 1.3 71.6 - - - +
136A PHE* 1.3 64.8 + - - +
137A ASN* 2.7 35.6 + - - +
6D G 3.0 50.2 + - - -
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Residues in contact with PHE 136 (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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39A VAL* 5.9 0.2 - - + -
41A LEU* 3.3 50.7 - - + -
44A ALA* 3.6 24.9 - - + -
52A GLN* 5.2 4.7 - - + -
54A PHE* 3.7 25.8 - + + -
78A ILE* 4.1 5.6 - - + -
98A ALA* 4.1 15.0 - - + -
99A THR 2.9 18.1 + - - +
100A LEU* 3.2 19.3 - - + +
101A VAL 2.8 26.0 + - - -
125A ALA* 4.6 4.9 - - + -
126A THR 3.1 15.9 - - - +
127A LEU* 3.8 24.2 - - + -
134A ARG* 4.5 1.8 - - + -
135A GLN* 1.3 73.9 - - - +
137A ASN* 1.3 62.0 + - - +
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Residues in contact with ASN 137 (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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100A LEU* 4.7 0.7 - - - -
101A VAL* 3.5 10.8 - - - +
103A TYR* 3.1 31.8 + - + -
125A ALA* 3.0 7.4 - - - +
126A THR* 2.7 42.0 + - - +
128A ARG* 3.7 14.1 - - - +
135A GLN* 2.7 40.3 + - - +
136A PHE* 1.3 75.6 - - - +
138A ALA* 1.3 62.0 + - - +
2D T 4.8 0.8 + - - -
4D T 3.3 25.4 - - + +
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Residues in contact with ALA 138 (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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100A LEU* 4.8 0.4 - - + -
101A VAL 3.2 6.3 + - - -
102A LEU* 3.6 25.2 - - + +
103A TYR* 2.9 28.0 + - - -
122A VAL* 4.1 15.0 - - + -
124A ARG 4.0 4.7 - - - +
125A ALA* 4.2 0.4 - - + -
137A ASN* 1.3 79.6 - - - +
139A ASN* 1.3 63.8 + - - +
140A VAL* 3.5 3.1 + - + +
144A SER* 3.8 20.9 - - - +
145A SER 5.7 0.2 - - - +
2D T 4.2 2.7 - - - -
4D T 4.8 0.6 + - - -
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Residues in contact with ASN 139 (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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103A TYR* 3.2 11.7 - - - +
138A ALA* 1.3 69.4 - - - +
140A VAL* 1.3 65.6 + - - +
141A PHE* 3.0 31.8 - - + -
142A TYR* 3.1 22.6 + - + +
143A SER 3.4 1.6 + - - -
144A SER* 3.1 22.5 + - - -
2D T 3.0 58.2 + - - +
3D T 4.0 0.2 + - - -
4D T 3.0 24.2 + - - +
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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