Contacts of the strand formed by residues 118 - 127 (chain I) in PDB entry 3KDO
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 VAL 118 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290E ARG* 3.0 32.3 + - - +
31I VAL* 4.2 22.2 - - + -
32I THR 3.5 7.2 - - - +
33I PRO* 4.4 0.2 - - - -
34I ALA* 4.1 0.9 - - - -
42I ALA* 4.2 9.4 - - + +
46I VAL* 4.2 7.2 - - + -
112I ILE 4.1 16.4 - - - +
115I MET* 3.3 30.9 - - + +
116I LYS 3.8 4.0 - - - +
117I ARG* 1.3 85.2 - - + +
119I LYS* 1.3 59.4 + - - +
120I GLY 4.0 10.8 - - - +
121I LEU* 4.4 12.6 - - + -
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Residues in contact with LYS 119 (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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290E ARG* 4.6 12.5 + - - +
32I THR* 2.6 32.6 + - + +
33I PRO 4.1 12.1 + - - +
34I ALA* 3.7 14.9 - - + +
35I GLU* 4.5 14.3 - - - +
118I VAL* 1.3 72.6 - - - +
120I GLY* 1.3 55.4 + - - +
294I HIS* 4.8 2.4 + - - +
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Residues in contact with GLY 120 (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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30I ARG 3.7 0.9 - - - +
31I VAL* 3.9 1.2 - - - -
32I THR* 3.0 33.6 + - - +
118I VAL* 3.3 7.4 - - - +
119I LYS* 1.3 82.2 - - - +
121I LEU* 1.3 61.8 + - - +
293I TYR* 3.4 17.9 - - - -
294I HIS* 3.7 11.9 - - - -
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Residues in contact with LEU 121 (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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29I PHE* 3.7 22.9 - - + -
30I ARG 3.6 0.7 - - - -
31I VAL* 3.7 31.2 - - + -
46I VAL* 4.0 18.4 - - + -
112I ILE* 3.4 56.3 - - + +
113I PHE* 3.2 23.1 - - + +
115I MET* 4.8 0.2 - - + -
118I VAL* 4.4 11.0 - - + -
120I GLY* 1.3 76.1 - - - +
122I ARG* 1.3 54.4 + - - +
293I TYR 3.4 1.0 + - - -
294I HIS* 3.1 11.4 + - - +
295I GLY 2.8 26.0 + - - -
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Residues in contact with ARG 122 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29I PHE* 3.3 4.3 - - - -
30I ARG* 2.8 51.2 + - + -
121I LEU* 1.3 73.7 - - - +
123I LEU* 1.3 73.3 + - - +
124I GLU* 3.0 33.9 + - - +
288I PHE 5.0 0.4 + - - -
289I THR 2.9 27.5 + - - -
290I ARG 4.7 1.0 + - - -
291I ASN 3.5 14.0 + - - +
292I PRO* 3.6 23.8 - - - +
293I TYR 3.9 2.9 - - - -
294I HIS 3.5 26.0 - - - +
295I GLY 3.3 5.5 - - - -
296I ILE 4.0 2.8 - - - -
297I SER* 3.5 28.9 + - - +
298I MET 4.8 0.4 - - - +
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Residues in contact with LEU 123 (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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27I ALA* 4.3 8.1 - - + -
28I VAL 3.7 6.3 - - - +
29I PHE* 3.6 31.9 - - + -
105I LEU* 5.4 0.9 - - + -
108I ILE* 3.7 31.6 - - + +
109I ALA* 4.1 10.1 - - + -
113I PHE* 4.1 7.9 - - + -
121I LEU 4.1 0.4 - - - -
122I ARG* 1.3 70.2 - - - +
124I GLU* 1.3 59.6 + - - +
125I ASP 3.6 21.1 - - - +
126I LEU* 4.5 4.5 - - + -
295I GLY 2.8 15.4 + - - +
296I ILE* 4.3 9.2 - - + -
297I SER* 2.9 26.2 + - - -
300I VAL* 3.7 27.1 - - + +
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Residues in contact with GLU 124 (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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28I VAL* 2.7 21.0 + - + +
29I PHE 4.3 1.6 - - - -
30I ARG* 3.4 34.5 + - + +
86I ILE* 4.8 1.1 - - + -
122I ARG* 3.0 43.0 + - - +
123I LEU* 1.3 73.9 - - - +
125I ASP* 1.3 61.1 + - - +
292I PRO 4.1 1.6 - - - +
297I SER* 3.7 7.1 + - - -
299I PHE* 3.6 24.3 - - - +
300I VAL* 3.8 2.0 - - - +
350I PHE* 3.6 49.0 - - + +
351I HIS* 3.9 6.4 + - - -
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Residues in contact with ASP 125 (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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26I ILE 4.4 0.4 - - - -
27I ALA* 3.6 1.2 - - - -
28I VAL* 3.0 34.2 + - + -
123I LEU* 3.6 9.5 - - - +
124I GLU* 1.3 81.4 - - - +
126I LEU* 1.3 81.7 + - - +
127I TYR* 4.2 1.7 - - - -
299I PHE* 3.3 28.2 - - + +
300I VAL* 3.7 10.9 - - - +
303I LYS* 3.4 21.5 + - - +
350I PHE 3.8 15.3 - - - +
352I LEU* 3.1 32.7 + - - +
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Residues in contact with LEU 126 (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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25I ILE* 4.3 11.4 - - + -
26I ILE 3.5 10.3 - - - +
27I ALA* 4.3 9.9 - - + -
101I LEU* 5.8 0.4 - - + -
104I LEU* 5.3 2.9 - - + -
105I LEU* 4.4 9.6 - - + -
108I ILE* 3.8 38.1 - - + -
123I LEU* 4.5 5.2 - - + -
125I ASP* 1.3 86.0 + - - +
127I TYR* 1.3 62.2 + - - +
128I PHE* 3.7 30.7 + - + -
300I VAL* 4.0 27.5 - - + +
303I LYS* 2.8 33.3 + - + +
304I LEU* 4.5 6.5 - - + -
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Residues in contact with TYR 127 (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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20I SER 4.9 0.2 - - - -
21I LYS* 2.7 45.0 + - + +
24I ASP 3.4 23.1 - - - -
25I ILE* 3.5 6.9 - - - +
26I ILE* 2.8 56.1 + - + +
125I ASP* 4.2 1.8 - - - -
126I LEU* 1.3 70.6 - - - +
128I PHE* 1.3 78.6 + - - +
129I PRO* 3.7 10.2 - - - +
130I GLU 5.1 0.3 + - - -
303I LYS* 4.3 1.8 - - - +
352I LEU* 4.0 17.2 - - + +
353I GLU 3.2 28.5 - - - -
354I GLN* 3.6 16.8 - - - +
355I LYS 5.3 1.6 - - - -
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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