Contacts of the strand formed by residues 98 - 104 (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 ALA 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A LEU* 4.6 2.2 - - + -
77A LYS* 3.4 3.5 - - - -
78A ILE* 2.7 44.8 + - + +
83A LEU* 3.7 20.1 - - + +
97A TYR* 1.3 77.2 - - - +
99A THR* 1.3 63.4 + - - +
133A GLN* 5.3 0.7 - - - +
134A ARG* 3.2 23.1 - - + +
136A PHE* 4.1 16.6 - - + -
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Residues in contact with THR 99 (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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75A SER* 5.7 2.2 - - - -
76A LEU 3.2 12.8 - - - +
77A LYS* 4.8 4.9 - - + -
78A ILE* 4.5 1.6 - - - -
97A TYR* 4.4 8.5 - - + -
98A ALA* 1.3 79.5 - - - +
100A LEU* 1.3 63.9 + - - +
101A VAL* 5.1 2.4 - - - +
130A TYR* 5.8 0.5 - - - -
133A GLN* 3.8 30.1 - - + +
134A ARG 3.0 6.6 + - - +
135A GLN* 3.2 31.0 + - - +
136A PHE* 2.9 28.3 + - - -
7D G 5.9 2.5 - - - +
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Residues in contact with LEU 100 (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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54A PHE* 4.2 11.9 - - + -
75A SER* 3.6 2.4 + - - -
76A LEU* 2.7 55.8 + - + +
78A ILE* 4.0 18.2 - - + -
99A THR* 1.3 75.4 - - - +
101A VAL* 1.3 64.8 + - - +
102A LEU* 3.9 26.2 - - + -
120A ILE* 4.2 16.8 - - + -
122A VAL* 3.9 24.2 - - + -
125A ALA* 5.2 0.2 - - + -
136A PHE* 3.2 31.6 - - + +
137A ASN* 4.4 4.3 - - - +
138A ALA* 4.8 1.8 - - + -
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Residues in contact with VAL 101 (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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73A ILE* 4.0 15.5 - - + -
74A CYS 3.7 2.5 - - - -
75A SER* 4.6 4.5 - - - +
99A THR* 5.1 2.5 - - - +
100A LEU* 1.3 77.9 - - - +
102A LEU* 1.3 62.4 + - - +
103A TYR* 3.4 33.6 - - + +
135A GLN* 4.1 25.6 - - + +
136A PHE 2.8 9.3 + - - -
137A ASN* 3.5 13.0 - - - +
138A ALA 3.2 22.2 + - - -
6D G 3.8 36.6 - - - +
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Residues in contact with LEU 102 (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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73A ILE* 3.4 9.5 - - - +
74A CYS* 2.9 32.4 + - + +
76A LEU* 4.1 18.8 - - + -
100A LEU* 3.9 18.6 - - + -
101A VAL* 1.3 73.5 - - - +
103A TYR* 1.3 62.3 + - - +
110A LEU* 3.8 14.3 - - + +
111A PRO* 3.5 36.8 - - + -
120A ILE* 4.4 6.3 - - + -
122A VAL* 4.7 8.5 - - + -
138A ALA* 3.6 27.6 - - + +
140A VAL* 4.8 6.1 - - + -
145A SER 5.9 0.4 - - - +
146A TRP* 4.1 17.9 - - + -
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Residues in contact with TYR 103 (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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71A ARG* 4.2 11.9 - - - +
72A TYR 3.6 3.4 - - - +
73A ILE* 3.8 29.2 - - + -
101A VAL* 3.4 27.6 - - + +
102A LEU* 1.3 74.4 - - - +
104A ALA* 1.3 59.9 + - - +
110A LEU* 4.1 1.1 - - - -
137A ASN* 3.1 28.7 + - - -
138A ALA 2.9 12.2 + - - -
139A ASN* 3.2 25.4 - - - +
140A VAL* 2.6 36.0 + - - +
141A PHE* 3.7 8.6 + - + -
4D T 3.6 41.9 - + + -
5D G 2.9 26.4 + - - -
6D G 4.3 1.6 + - - -
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Residues in contact with ALA 104 (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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71A ARG* 3.6 6.4 + - - +
72A TYR* 2.7 33.5 + - - +
103A TYR* 1.3 77.1 - - - +
105A LYS* 1.3 61.4 + - - +
106A ARG 3.4 17.7 - - - +
109A ASP* 3.7 17.3 - - + +
110A LEU* 3.6 23.6 - - + -
140A VAL* 4.2 3.6 - - + -
141A PHE* 4.0 10.1 - - - +
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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