Contacts of the strand formed by residues 101 - 109 (chain I) in PDB entry 1K9O
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 101 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99I ASP* 3.3 24.9 + - - +
100I LEU* 1.3 78.9 - - - +
102I MET* 1.3 62.2 + - - +
103I ALA* 3.9 0.4 + - - -
152I GLN 3.8 15.9 - - - +
153I THR* 3.6 23.6 + - + +
154I ASN* 2.9 41.4 + - - +
156I ARG* 5.3 1.0 - - - +
177I ALA 3.2 3.5 - - - +
178I ILE* 3.1 7.1 - - - -
179I TYR* 2.9 61.0 + - + -
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Residues in contact with MET 102 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46I SER* 4.0 3.1 - - - +
48I PHE* 3.7 19.3 - - + -
49I SER* 3.6 30.5 - - - -
92I VAL* 6.3 2.9 - - + -
100I LEU* 3.4 29.1 + - + -
101I LYS* 1.3 71.3 - - - +
103I ALA* 1.3 59.5 + - - +
152I GLN* 5.2 3.6 + - - -
177I ALA 3.5 2.2 - - - -
178I ILE* 3.7 21.8 - - + -
378I MET* 3.2 37.7 - - + -
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Residues in contact with ALA 103 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49I SER* 5.4 0.8 - - - -
101I LYS 5.5 0.2 - - - -
102I MET* 1.3 75.3 - - - +
104I SER* 1.3 70.4 + - - +
148I TRP* 4.1 18.6 - - + -
149I VAL* 5.8 0.9 - - - -
152I GLN* 4.1 24.9 - - + +
153I THR* 5.2 3.1 - - + -
176I ASN* 2.8 17.5 + - - +
177I ALA* 2.7 36.5 + - + +
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Residues in contact with SER 104 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49I SER* 3.5 5.6 + - - -
52I PRO* 6.0 0.9 - - - -
53I PRO* 3.2 35.2 - - - +
56I GLN* 5.5 4.3 - - - -
103I ALA* 1.3 82.3 + - - +
105I LYS* 1.3 63.4 + - - +
128I SER* 3.4 21.7 - - - -
148I TRP* 3.7 9.3 - - - -
174I LEU* 5.1 0.7 - - - -
175I VAL 3.4 9.0 - - - -
176I ASN* 3.1 14.7 + - - +
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Residues in contact with LYS 105 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56I GLN* 5.8 1.3 - - - +
104I SER* 1.3 75.2 - - - +
106I ILE* 1.3 71.0 + - - +
107I TYR* 3.5 28.7 - - + -
128I SER* 4.7 3.1 - - - -
129I GLU* 2.9 61.2 + - - +
131I GLN* 4.2 16.2 - - + +
148I TRP* 3.3 49.2 - - + +
173I VAL 3.7 1.0 - - - +
174I LEU* 3.6 8.0 - - - +
175I VAL* 3.1 33.6 + - + +
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Residues in contact with ILE 106 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56I GLN* 4.3 27.3 + - + +
57I LEU* 3.3 36.3 - - + -
105I LYS* 1.3 80.9 - - - +
107I TYR* 1.3 65.4 + - - +
108I VAL* 4.1 15.0 - - + -
128I SER* 5.7 0.4 + - - -
129I GLU 4.1 3.6 + - - +
130I VAL* 3.7 26.7 - - + +
131I GLN* 2.9 27.4 + - - +
172I SER* 4.8 6.7 - - - -
173I VAL 3.6 7.9 - - - +
174I LEU* 4.2 15.9 - - + -
315I LEU* 4.7 10.8 - - + -
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Residues in contact with TYR 107 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105I LYS* 3.5 24.5 - - + -
106I ILE* 1.3 74.6 - - - +
108I VAL* 1.3 62.9 + - - +
131I GLN* 3.0 41.3 + - + +
133I VAL* 3.9 16.8 - - + -
135I PHE* 3.1 20.9 - - + -
144I ALA 4.9 2.0 - - - -
145I ILE* 3.9 36.9 - - + -
148I TRP* 3.3 37.4 - - - +
172I SER* 3.1 23.9 - - - -
173I VAL* 3.1 15.0 + - + +
175I VAL* 3.5 29.6 - - + -
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Residues in contact with VAL 108 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106I ILE* 4.1 17.7 - - + -
107I TYR* 1.3 77.0 - - - +
109I ALA* 1.3 68.1 + - - +
112I LEU* 3.9 11.9 - - + -
114I LEU* 3.6 28.9 - - + -
130I VAL* 4.3 3.6 - - + -
131I GLN 2.8 17.9 + - - +
132I ASN* 2.9 40.4 - - - +
133I VAL 3.2 2.2 + - - -
135I PHE* 3.9 2.0 - - - -
171I ARG 3.3 5.8 - - - +
172I SER* 4.2 2.7 - - - -
315I LEU* 4.1 8.7 - - + -
322I LEU* 4.1 24.9 - - + -
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Residues in contact with ALA 109 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108I VAL* 1.3 73.2 - - - +
110I LYS* 1.3 66.2 + - - +
111I GLY* 2.9 4.2 + - - +
112I LEU* 3.1 19.8 + - + +
132I ASN* 3.1 8.8 + - - -
133I VAL 3.5 2.7 - - - +
135I PHE* 3.4 25.7 - - + -
168I GLU* 4.1 24.0 - - + +
170I THR 4.0 9.6 - - - +
171I ARG* 3.0 17.0 + - - +
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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