Contacts of the strand formed by residues 118 - 127 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A VAL* 4.1 24.2 - - + -
32A THR 3.6 7.4 - - - +
34A ALA* 3.7 4.3 - - - +
42A ALA* 4.7 8.5 - - + +
45A ALA* 6.2 0.4 - - + -
46A VAL* 4.5 17.0 - - + -
112A ILE 4.2 7.2 - - - +
113A PHE 4.8 1.1 - - - +
115A MET* 2.6 50.2 - - + +
116A LYS 2.4 30.3 + - - +
117A ARG* 1.3 80.8 - - + +
119A LYS* 1.3 59.3 + - - +
120A GLY 4.4 4.9 - - - +
121A LEU* 4.6 14.8 - - + +
294A HIS* 6.2 0.4 - - + -
290H ARG* 3.5 14.8 + - - +
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Residues in contact with LYS 119 (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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32A THR* 2.8 26.2 + - + +
33A PRO 4.1 6.3 - - - +
34A ALA* 3.9 6.2 - - + +
118A VAL* 1.3 76.5 - - - +
120A GLY* 1.3 58.7 + - - +
294A HIS* 4.5 5.0 + - - -
290H ARG* 4.8 12.2 + - - +
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Residues in contact with GLY 120 (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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30A ARG 3.6 4.2 - - - +
32A THR* 3.0 35.1 + - - -
118A VAL* 3.7 2.6 - - - +
119A LYS* 1.3 81.4 - - - +
121A LEU* 1.3 58.0 + - - -
293A TYR* 3.2 23.7 - - - +
294A HIS* 3.6 9.2 - - - -
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Residues in contact with LEU 121 (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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29A PHE* 3.6 33.4 - - + -
30A ARG 4.0 0.7 - - - +
31A VAL* 4.0 18.4 - - + -
46A VAL* 4.0 17.7 - - + -
112A ILE* 3.4 57.9 - - + +
113A PHE* 3.5 18.3 - - + +
115A MET* 4.4 0.4 - - + -
118A VAL* 4.6 11.3 - - + +
120A GLY* 1.3 72.5 - - - -
122A ARG* 1.3 64.8 + - - +
294A HIS* 3.0 15.2 + - + +
295A GLY 2.9 19.4 + - - -
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Residues in contact with ARG 122 (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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29A PHE* 3.5 4.3 - - - -
30A ARG* 2.9 39.8 + - + +
121A LEU* 1.3 75.2 - - - +
123A LEU* 1.3 62.5 + - - +
124A GLU* 2.8 33.3 + - - +
289A THR 3.8 14.5 + - - -
290A ARG 5.7 0.4 - - - -
291A ASN 3.3 18.5 + - - -
292A PRO* 2.8 39.3 + - - +
293A TYR 3.7 3.6 - - - -
294A HIS* 3.5 16.7 + - - +
295A GLY 3.5 4.0 - - - +
296A ILE 3.9 3.8 + - - -
297A SER* 3.3 45.6 + - - +
298A MET 5.1 0.2 - - - +
329A ILE* 6.2 2.2 - - - +
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Residues in contact with LEU 123 (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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27A ALA* 4.2 3.8 - - + -
28A VAL 3.5 9.2 - - - +
29A PHE* 3.7 31.9 - - + -
105A LEU* 5.7 1.3 - - + -
108A ILE* 4.2 15.3 - - + +
109A ALA* 4.3 13.7 - - + -
113A PHE* 4.4 4.1 - - + -
121A LEU 4.3 0.4 - - - -
122A ARG* 1.3 68.8 - - - +
124A GLU* 1.3 60.6 + - - +
125A ASP 3.1 28.7 - - - +
126A LEU* 4.2 18.2 - - + -
295A GLY 3.1 13.5 + - - +
296A ILE* 4.5 12.6 - - + -
297A SER* 3.1 25.3 + - - -
300A VAL* 3.7 24.0 - - + +
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Residues in contact with GLU 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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28A VAL* 2.7 28.7 + - + +
30A ARG* 3.2 30.0 - - + +
86A ILE* 5.7 1.3 - - + -
122A ARG* 2.8 55.1 + - - +
123A LEU* 1.3 74.0 - - - +
125A ASP* 1.3 59.8 + - - +
292A PRO 3.9 1.9 - - - +
297A SER* 3.7 7.1 + - - -
299A PHE* 3.7 24.8 - - - +
300A VAL* 3.9 2.6 - - - +
350A PHE* 3.9 35.4 - - + +
351A HIS* 4.5 4.0 + - - -
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Residues in contact with ASP 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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26A ILE 4.3 0.2 - - - -
27A ALA* 3.3 1.0 - - - -
28A VAL* 2.9 32.7 + - + -
123A LEU* 3.1 15.2 - - - +
124A GLU* 1.3 82.0 - - - +
126A LEU* 1.3 95.8 + - - +
127A TYR* 4.3 1.1 - - - -
299A PHE* 3.4 26.8 - - + -
300A VAL* 3.9 8.3 - - - +
303A LYS* 3.4 12.6 + - - -
350A PHE 3.9 15.0 - - - +
351A HIS* 3.7 0.2 - - - -
352A LEU* 3.3 30.3 + - - +
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Residues in contact with LEU 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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25A ILE* 4.5 10.5 - - + -
26A ILE 3.3 4.0 - - - +
27A ALA* 3.4 26.7 - - + +
101A LEU* 6.0 0.2 - - + -
104A LEU* 5.1 0.2 - - + -
105A LEU* 4.6 9.4 - - + -
108A ILE* 2.5 43.3 - - + -
123A LEU* 4.2 9.6 - - + -
125A ASP* 1.3 88.8 + - - +
127A TYR* 1.3 56.5 + - - +
128A PHE* 3.8 21.7 + - + -
300A VAL* 4.3 23.0 - - + +
303A LYS* 2.6 38.9 + - - +
304A LEU* 4.8 7.4 - - + -
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Residues in contact with TYR 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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20A SER 4.8 0.7 - - - -
21A LYS* 2.9 41.4 + - + +
24A ASP 3.7 18.2 - - - -
25A ILE* 3.2 19.2 - - - +
26A ILE* 2.5 42.2 + - + +
125A ASP* 4.8 0.6 - - - -
126A LEU* 1.3 71.9 - - - +
128A PHE* 1.3 73.2 + - - +
129A PRO* 3.7 14.8 - - - +
130A GLU 5.2 0.5 + - - -
303A LYS* 4.2 1.1 - - - +
352A LEU* 4.3 16.1 - - + +
353A GLU* 3.2 30.7 - - + -
354A GLN* 3.5 19.7 - - - +
355A LYS 5.4 0.9 - - - -
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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